Research related to RNA


Advertisements
Advertisements

Research Summary: RNA Captor: A Tool for RNA Characterization

 2 total views

ABSTRACT Background In the genome era, characterizing the structure and the function of RNA molecules remains a major challenge. Alternative transcripts and non-protein-coding genes are poorly recognized by the current genome-annotation algorithms and efficient tools are needed to isolate the less-abundant or stable RNAs. Results A universal RNA-tagging method using the T4 RNA ligase 2 … Continue readingResearch Summary: RNA Captor: A Tool for RNA Characterization

Research Summary: Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis

 1 total views

ABSTRACT RNA silencing functions as an important antiviral defense mechanism in a broad range of eukaryotes. In plants, biogenesis of several classes of endogenous small interfering RNAs (siRNAs) requires RNA-dependent RNA Polymerase (RDR) activities. Members of the RDR family proteins, including RDR1and RDR6, have also been implicated in antiviral defense, although a direct role for … Continue readingResearch Summary: Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis

Research Summary: Functional lability of RNA-dependent RNA polymerases in animals

 0 total views

ABSTRACT RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in … Continue readingResearch Summary: Functional lability of RNA-dependent RNA polymerases in animals

Research Summary: Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching

 0 total views

Abstract The investigation of RNA-based regulation of cellular processes is becoming an increasingly important part of biological or medical research. For the analysis of this type of data, RNA-related prediction tools are integrated into many pipelines and workflows. In order to correctly apply and tune these programs, the user has to have a precise understanding … Continue readingResearch Summary: Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching

Research Summary: RNA Silencing Sheds Light on the RNA World

 0 total views

Abstract ____________________________ Publisher: Public Library of Science Author(s): Jones R. Link: https://doi.org/10.1371/journal.pbio.0040448

Research Summary: Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families

 0 total views

ABSTRACT The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion/deletion, and by mutations that … Continue readingResearch Summary: Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families

Research Summary: Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction

 2 total views

ABSTRACT Evidence is accumulating in support of the functional importance of subcellular RNA localization in diverse biological contexts. In different cell types, distinct RNA localization patterns are frequently observed, and the available data indicate that this is achieved through a series of highly coordinated events. Classically, cis–elements within the RNA to be localized are recognized … Continue readingResearch Summary: Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction

Research Summary: Engineered Picornavirus VPg-RNA Substrates: Analysis of a Tyrosyl-RNA Phosphodiesterase Activity

 0 total views

ABSTRACT Using poliovirus, the prototypic member of Picornaviridae, we have further characterized a host cell enzymatic activity found in uninfected cells, termed “unlinkase,” that recognizes and cleaves the unique 5′ tyrosyl-RNA phosphodiester bond found at the 5′ end of picornavirus virion RNAs. This bond connects VPg, a viral-encoded protein primer essential for RNA replication, to … Continue readingResearch Summary: Engineered Picornavirus VPg-RNA Substrates: Analysis of a Tyrosyl-RNA Phosphodiesterase Activity

Research Summary: Exploration of Small RNAs

 0 total views

Abstract For several decades, only a limited number of noncoding RNAs, such as ribosomal and transfer RNA, have been studied in any depth. In recent years, additional species of noncoding RNAs have increasingly been discovered. Of these, small RNA species attract particular interest because of their essential roles in processes such as RNA silencing and … Continue readingResearch Summary: Exploration of Small RNAs

Research Summary: Who Watches the Watchmen: Roles of RNA Modifications in the RNA Interference Pathway

 0 total views

ABSTRACT RNA levels are widely thought to be predictive of RNA function. However, the existence of more than a hundred chemically distinct modifications of RNA alone is a major indication that these moieties may impart distinct functions to subgroups of RNA molecules that share a primary sequence but display distinct RNA “epigenetic” marks. RNAs can … Continue readingResearch Summary: Who Watches the Watchmen: Roles of RNA Modifications in the RNA Interference Pathway

Research Summary: Small Cofactors May Assist Protein Emergence from RNA World: Clues from RNA-Protein Complexes

 

ABSTRACT It is now widely accepted that at an early stage in the evolution of life an RNA world arose, in which RNAs both served as the genetic material and catalyzed diverse biochemical reactions. Then, proteins have gradually replaced RNAs because of their superior catalytic properties in catalysis over time. Therefore, it is important to … Continue readingResearch Summary: Small Cofactors May Assist Protein Emergence from RNA World: Clues from RNA-Protein Complexes

Research Summary: Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

 

Abstract The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions. Unfortunately, intra- and inter-molecular base-pairing information is lacking for most RNAs. Here, we marry classical nuclease-based structure … Continue readingResearch Summary: Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

RNA polymerase fosters splicing and inhibits degradation

 

Author: Benison P. Zerrudo RNA’s future is undetermined as it exits the DNA assembly process. One route leads to further processing and, eventually, protein translation. However, down the other is oblivion, degradation by RNA-digesting enzymes and recycling back into the original nucleotides. According to a recent study by Martin Hicks, Klemens Hertel, and others, a … Continue readingRNA polymerase fosters splicing and inhibits degradation

Research Abstract: Hyperexpansion of RNA Bacteriophage Diversity

 

Abstract Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the limited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that … Continue readingResearch Abstract: Hyperexpansion of RNA Bacteriophage Diversity

Research Abstract: The DNA/RNA-Dependent RNA Polymerase QDE-1 Generates Aberrant RNA and dsRNA for RNAi in a Process Requiring Replication Protein A and a DNA Helicase

 

Abstract The Neurospora RNA-dependent RNA polymerase QDE-1 is an RNA polymerase that can use both RNA and DNA as templates, suggesting a new mechanism for small RNA production. ____________________________ Publisher: Public Library of Science Date Published: 5-October-2010 Author(s): Lee H., Aalto A., Yang Q., Chang S., Huang G., Fisher D., Cha J., Poranen M., Bamford … Continue readingResearch Abstract: The DNA/RNA-Dependent RNA Polymerase QDE-1 Generates Aberrant RNA and dsRNA for RNAi in a Process Requiring Replication Protein A and a DNA Helicase

Research Summary: Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson’s Leukocytes Identified by RNA Sequencing

 

Abstract The continuously prolonged human lifespan is accompanied by increase in neurodegenerative diseases incidence, calling for the development of inexpensive blood-based diagnostics. Analyzing blood cell transcripts by RNA-Seq is a robust means to identify novel biomarkers that rapidly becomes a commonplace. However, there is lack of tools to discover novel exons, junctions and splicing events … Continue readingResearch Summary: Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson’s Leukocytes Identified by RNA Sequencing

Research Summary: Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

 

Abstract Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial … Continue readingResearch Summary: Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

Research Summary: Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo

 

ABSTRACT The RNA helicase SUV3 and the polynucleotide phosphorylase PNPase are involved in the degradation of mitochondrial mRNAs but their roles in vivo are not fully understood. Additionally, upstream processes, such as transcript maturation, have been linked to some of these factors, suggesting either dual roles or tightly interconnected mechanisms of mitochondrial RNA metabolism. To … Continue readingResearch Summary: Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo

Research Summary: EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame

 

Abstract Emerging RNA-based approaches to disease detection and gene therapy require RNA sequences that fold into specific base-pairing patterns, but computational algorithms generally remain inadequate for these secondary structure design tasks. The Eterna project has crowdsourced RNA design to human video game players in the form of puzzles that reach extraordinary difficulty. Here, we demonstrate … Continue readingResearch Summary: EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame

Research Summary: Nicotiana Small RNA Sequences Support a Host Genome Origin of Cucumber Mosaic Virus Satellite RNA

 

ABSTRACT Satellite RNAs (satRNAs) are small noncoding subviral RNA pathogens in plants that depend on helper viruses for replication and spread. Despite many decades of research, the origin of satRNAs remains unknown. In this study we show that a β-glucuronidase (GUS) transgene fused with a Cucumber mosaic virus (CMV) Y satellite RNA (Y-Sat) sequence (35S-GUS:Sat) … Continue readingResearch Summary: Nicotiana Small RNA Sequences Support a Host Genome Origin of Cucumber Mosaic Virus Satellite RNA

Research Summary: Extragenic Accumulation of RNA Polymerase II Enhances Transcription by RNA Polymerase III

 

Abstract Recent genomic data indicate that RNA polymerase II (Pol II) function extends beyond conventional transcription of primarily protein-coding genes. Among the five snRNAs required for pre-mRNA splicing, only the U6 snRNA is synthesized by RNA polymerase III (Pol III). Here we address the question of how Pol II coordinates the expression of spliceosome components, … Continue readingResearch Summary: Extragenic Accumulation of RNA Polymerase II Enhances Transcription by RNA Polymerase III

Research Summary: Genomic HIV RNA Induces Innate Immune Responses through RIG-I-Dependent Sensing of Secondary-Structured RNA

 

ABSTRACT Background Innate immune responses have recently been appreciated to play an important role in the pathogenesis of HIV infection. Whereas inadequate innate immune sensing of HIV during acute infection may contribute to failure to control and eradicate infection, persistent inflammatory responses later during infection contribute in driving chronic immune activation and development of immunodeficiency. … Continue readingResearch Summary: Genomic HIV RNA Induces Innate Immune Responses through RIG-I-Dependent Sensing of Secondary-Structured RNA

Research Summary: Epigenetic Regulation by Heritable RNA

 

ABSTRACT Genomic concepts are based on the assumption that phenotypes arise from the expression of genetic variants. However, the presence of non-Mendelian inheritance patterns provides a direct challenge to this view and suggests an important role for alternative mechanisms of gene regulation and inheritance. Over the past few years, a highly complex and diverse network … Continue readingResearch Summary: Epigenetic Regulation by Heritable RNA

Research Summary: Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure

 

Abstract The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 Å resolution. The structure contains the full complement … Continue readingResearch Summary: Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure

Research Summary: Viral Suppressors of RNA Silencing Hinder Exogenous and Endogenous Small RNA Pathways in Drosophila

 

ABSTRACT Background In plants and insects, RNA interference (RNAi) is the main responder against viruses and shapes the basis of antiviral immunity. Viruses counter this defense by expressing viral suppressors of RNAi (VSRs). While VSRs in Drosophila melanogaster were shown to inhibit RNAi through different modes of action, whether they act on other silencing pathways … Continue readingResearch Summary: Viral Suppressors of RNA Silencing Hinder Exogenous and Endogenous Small RNA Pathways in Drosophila

Research Summary: The RNA Silencing Enzyme RNA Polymerase V Is Required for Plant Immunity

 

Abstract RNA–directed DNA methylation (RdDM) is an epigenetic control mechanism driven by small interfering RNAs (siRNAs) that influence gene function. In plants, little is known of the involvement of the RdDM pathway in regulating traits related to immune responses. In a genetic screen designed to reveal factors regulating immunity in Arabidopsis thaliana, we identified NRPD2 … Continue readingResearch Summary: The RNA Silencing Enzyme RNA Polymerase V Is Required for Plant Immunity

Research Summary: Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

 

ABSTRACT Many computational methods have been used to predict novel non-coding RNAs (ncRNAs), but none, to our knowledge, have explicitly investigated the impact of integrating existing cDNA-based Expressed Sequence Tag (EST) data that flank structural RNA predictions. To determine whether flanking EST data can assist in microRNA (miRNA) prediction, we identified genomic sites encoding putative … Continue readingResearch Summary: Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

Research Summary: Comparison of Dengue Virus Type 2-Specific Small RNAs from RNA Interference-Competent and –Incompetent Mosquito Cells

 

ABSTRACT The exogenous RNA interference (RNAi) pathway is an important antiviral defense against arboviruses in mosquitoes, and virus-specific small interfering (si)RNAs are key components of this pathway. Understanding the biogenesis of siRNAs in mosquitoes could have important ramifications in using RNAi to control arbovirus transmission. Using deep sequencing technology, we characterized dengue virus type 2 … Continue readingResearch Summary: Comparison of Dengue Virus Type 2-Specific Small RNAs from RNA Interference-Competent and –Incompetent Mosquito Cells

Research Summary: Global Array-Based Transcriptomics from Minimal Input RNA Utilising an Optimal RNA Isolation Process Combined with SPIA cDNA Probes

 

ABSTRACT Background Technical advances in the collection of clinical material, such as laser capture microdissection and cell sorting, provide the advantage of yielding more refined and homogenous populations of cells. However, these attractive advantages are counter balanced by the significant difficultly in obtaining adequate nucleic acid yields to allow transcriptomic analyses. Established technologies are available … Continue readingResearch Summary: Global Array-Based Transcriptomics from Minimal Input RNA Utilising an Optimal RNA Isolation Process Combined with SPIA cDNA Probes

Research Summary: The Impact of mRNA Structure on Guide RNA Targeting in Kinetoplastid RNA Editing

 

ABSTRACT Mitochondrial mRNA editing in Trypanosoma brucei requires the specific interaction of a guide RNA with its cognate mRNA. Hundreds of gRNAs are involved in the editing process, each needing to target their specific editing domain within the target message. We hypothesized that the structure surrounding the mRNA target may be a limiting factor and … Continue readingResearch Summary: The Impact of mRNA Structure on Guide RNA Targeting in Kinetoplastid RNA Editing

Research Summary: Sets of RNA Repeated Tags and Hybridization-Sensitive Fluorescent Probes for Distinct Images of RNA in a Living Cell

 

ABSTRACT Background Imaging the behavior of RNA in a living cell is a powerful means for understanding RNA functions and acquiring spatiotemporal information in a single cell. For more distinct RNA imaging in a living cell, a more effective chemical method to fluorescently label RNA is now required. In addition, development of the technology labeling … Continue readingResearch Summary: Sets of RNA Repeated Tags and Hybridization-Sensitive Fluorescent Probes for Distinct Images of RNA in a Living Cell

Research Summary: Inhibition of RNA Recruitment and Replication of an RNA Virus by Acridine Derivatives with Known Anti-Prion Activities

 

ABSTRACT Background Small molecule inhibitors of RNA virus replication are potent antiviral drugs and useful to dissect selected steps in the replication process. To identify antiviral compounds against Tomato bushy stunt virus (TBSV), a model positive stranded RNA virus, we tested acridine derivatives, such as chlorpromazine (CPZ) and quinacrine (QC), which are active against prion-based … Continue readingResearch Summary: Inhibition of RNA Recruitment and Replication of an RNA Virus by Acridine Derivatives with Known Anti-Prion Activities

Research Summary: Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

 

ABSTRACT mRNA half-lives are transcript-specific and vary over a range of more than 100-fold in eukaryotic cells. mRNA stabilities can be regulated by sequence-specific RNA-binding proteins (RBPs), which bind to regulatory sequence elements and modulate the interaction of the mRNA with the cellular RNA degradation machinery. However, it is unclear if this kind of regulation … Continue readingResearch Summary: Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

Research Summary: Identification of Widespread Ultra-Edited Human RNAs

 

Abstract Adenosine-to-inosine modification of RNA molecules (A-to-I RNA editing) is an important mechanism that increases transciptome diversity. It occurs when a genomically encoded adenosine (A) is converted to an inosine (I) by ADAR proteins. Sequencing reactions read inosine as guanosine (G); therefore, current methods to detect A-to-I editing sites align RNA sequences to their corresponding … Continue readingResearch Summary: Identification of Widespread Ultra-Edited Human RNAs

Research Summary: RNA-Binding Protein FXR1 Regulates p21 and TERC RNA to Bypass p53-Mediated Cellular Senescence in OSCC

 

ABSTRACT RNA-binding proteins (RBP) regulate numerous aspects of co- and post-transcriptional gene expression in cancer cells. Here, we demonstrate that RBP, fragile X-related protein 1 (FXR1), plays an essential role in cellular senescence by utilizing mRNA turnover pathway. We report that overexpressed FXR1 in head and neck squamous cell carcinoma targets (G-quadruplex (G4) RNA structure … Continue readingResearch Summary: RNA-Binding Protein FXR1 Regulates p21 and TERC RNA to Bypass p53-Mediated Cellular Senescence in OSCC

Research Summary: Template-Based Modeling of Protein-RNA Interactions

 

Abstract Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although … Continue readingResearch Summary: Template-Based Modeling of Protein-RNA Interactions

Research Summary: Potent Host-Directed Small-Molecule Inhibitors of Myxovirus RNA-Dependent RNA-Polymerases

 

ABSTRACT Therapeutic targeting of host cell factors required for virus replication rather than of pathogen components opens new perspectives to counteract virus infections. Anticipated advantages of this approach include a heightened barrier against the development of viral resistance and a broadened pathogen target spectrum. Myxoviruses are predominantly associated with acute disease and thus are particularly … Continue readingResearch Summary: Potent Host-Directed Small-Molecule Inhibitors of Myxovirus RNA-Dependent RNA-Polymerases

Research Summary: Evolutionary Triplet Models of Structured RNA

 

Abstract The reconstruction and synthesis of ancestral RNAs is a feasible goal for paleogenetics. This will require new bioinformatics methods, including a robust statistical framework for reconstructing histories of substitutions, indels and structural changes. We describe a “transducer composition” algorithm for extending pairwise probabilistic models of RNA structural evolution to models of multiple sequences related … Continue readingResearch Summary: Evolutionary Triplet Models of Structured RNA

Research Summary: Sequence-Specific Inhibition of Small RNA Function

 

Abstract Hundreds of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) have been identified from both plants and animals, yet little is known about their biochemical modes of action or biological functions. Here we report that 2′-O-methyl oligonucleotides can act as irreversible, stoichiometric inhibitors of small RNA function. We show that a 2′-O-methyl oligonucleotide complementary … Continue readingResearch Summary: Sequence-Specific Inhibition of Small RNA Function

Research Summary: Comparison of Insertional RNA Editing in Myxomycetes

 

Abstract RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA … Continue readingResearch Summary: Comparison of Insertional RNA Editing in Myxomycetes

Research Summary: Accurate Strand-Specific Quantification of Viral RNA

 

ABSTRACT The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR) assays are increasingly being … Continue readingResearch Summary: Accurate Strand-Specific Quantification of Viral RNA

Research Summary: Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

 

Abstract RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not … Continue readingResearch Summary: Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

Research Summary: Ribonucleoprotein Particles Containing Non-Coding Y RNAs, Ro60, La and Nucleolin Are Not Required for Y RNA Function in DNA Replication

 

ABSTRACT Background Ro ribonucleoprotein particles (Ro RNPs) consist of a non-coding Y RNA bound by Ro60, La and possibly other proteins. The physiological function of Ro RNPs is controversial as divergent functions have been reported for its different constituents. We have recently shown that Y RNAs are essential for the initiation of mammalian chromosomal DNA … Continue readingResearch Summary: Ribonucleoprotein Particles Containing Non-Coding Y RNAs, Ro60, La and Nucleolin Are Not Required for Y RNA Function in DNA Replication

Research Summary: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements

 

ABSTRACT Background There are currently no vaccines or antivirals available for dengue virus infection, which can cause dengue hemorrhagic fever and death. A better understanding of the host pathogen interaction is required to develop effective therapies to treat DENV. In particular, very little is known about how cellular RNA binding proteins interact with viral RNAs. … Continue readingResearch Summary: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements

Research Summary: Transcription of the Major Neurospora crassa microRNA–Like Small RNAs Relies on RNA Polymerase III

 

Abstract Most plant and animal microRNAs (miRNAs) are transcribed by RNA polymerase II. We previously discovered miRNA–like small RNAs (milRNAs) in the filamentous fungus Neurospora crassa and uncovered at least four different pathways for milRNA production. To understand the evolutionary origin of milRNAs, we determined the roles of polymerases II and III (Pol II and … Continue readingResearch Summary: Transcription of the Major Neurospora crassa microRNA–Like Small RNAs Relies on RNA Polymerase III

Research Summary: A Probabilistic Model of RNA Conformational Space

 

Abstract The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling procedure. Both are only partly solved problems. … Continue readingResearch Summary: A Probabilistic Model of RNA Conformational Space

Research Summary: Cell-Type Specific Features of Circular RNA Expression

 

Abstract Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account … Continue readingResearch Summary: Cell-Type Specific Features of Circular RNA Expression

Research Summary: Classifying RNA-Binding Proteins Based on Electrostatic Properties

 

Abstract Protein structure can provide new insight into the biological function of a protein and can enable the design of better experiments to learn its biological roles. Moreover, deciphering the interactions of a protein with other molecules can contribute to the understanding of the protein’s function within cellular processes. In this study, we apply a … Continue readingResearch Summary: Classifying RNA-Binding Proteins Based on Electrostatic Properties

Research Summary: Pseudoknots: RNA Structures with Diverse Functions

 

Abstract Just as proteins form distinct structural motifs, certain structures are commonly adopted by RNA molecules. Amongst the most prevalent is the RNA pseudoknot. ____________________________ Publisher: Public Library of Science Author(s): Staple D., Butcher S. Link: https://doi.org/10.1371/journal.pbio.0030213

Research Summary: Short RNA Guides Cleavage by Eukaryotic RNase III

 

ABSTRACT In eukaryotes, short RNAs guide a variety of enzymatic activities that range from RNA editing to translation repression. It is hypothesized that pre-existing proteins evolved to bind and use guide RNA during evolution. However, the capacity of modern proteins to adopt new RNA guides has never been demonstrated. Here we show that Rnt1p, the … Continue readingResearch Summary: Short RNA Guides Cleavage by Eukaryotic RNase III

Research Summary: Modeling Recursive RNA Interference

 

Abstract An important application of the RNA interference (RNAi) pathway is its use as a small RNA-based regulatory system commonly exploited to suppress expression of target genes to test their function in vivo. In several published experiments, RNAi has been used to inactivate components of the RNAi pathway itself, a procedure termed recursive RNAi in … Continue readingResearch Summary: Modeling Recursive RNA Interference

Research Summary: RNA Folding and Catalysis Mediated by Iron (II)

 

ABSTRACT Mg2+ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe2+ in the absence of free oxygen as a replacement for Mg2+ in RNA folding and catalysis. We describe both quantum mechanical calculations and … Continue readingResearch Summary: RNA Folding and Catalysis Mediated by Iron (II)

Research Summary: Ccr4-Not Regulates RNA Polymerase I Transcription and Couples Nutrient Signaling to the Control of Ribosomal RNA Biogenesis

 

ABSTRACT Ribosomal RNA synthesis is controlled by nutrient signaling through the mechanistic target of rapamycin complex 1 (mTORC1) pathway. mTORC1 regulates ribosomal RNA expression by affecting RNA Polymerase I (Pol I)-dependent transcription of the ribosomal DNA (rDNA) but the mechanisms involved remain obscure. This study provides evidence that the Ccr4-Not complex, which regulates RNA Polymerase … Continue readingResearch Summary: Ccr4-Not Regulates RNA Polymerase I Transcription and Couples Nutrient Signaling to the Control of Ribosomal RNA Biogenesis

Research Summary: RNA Modulators of Complex Phenotypes in Mammalian Cells

 

ABSTRACT RNA-mediated gene silencing, in the form of RNA interference (RNAi) or microRNAs (miRNAs) has provided novel tools for gene discovery and validation in mammalian cells. Here, we report on the construction and application of a random small RNA expression library for use in identifying small interfering RNA (siRNA) effectors that can modify complex cellular … Continue readingResearch Summary: RNA Modulators of Complex Phenotypes in Mammalian Cells

Research Summary: What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus?

 

Abstract Poliovirus (PV) is a well-characterized RNA virus, and the RNA-dependent RNA polymerase (RdRp) from PV (3Dpol) has been widely employed as an important model for understanding the structure-function relationships of RNA and DNA polymerases. Many experimental studies of the kinetics of nucleotide incorporation by RNA and DNA polymerases suggest that each nucleotide incorporation cycle … Continue readingResearch Summary: What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus?

Research Summary: Coarse-Grained Prediction of RNA Loop Structures

 

ABSTRACT One of the key issues in the theoretical prediction of RNA folding is the prediction of loop structure from the sequence. RNA loop free energies are dependent on the loop sequence content. However, most current models account only for the loop length-dependence. The previously developed “Vfold” model (a coarse-grained RNA folding model) provides an … Continue readingResearch Summary: Coarse-Grained Prediction of RNA Loop Structures

Research Summary: Is Thermosensing Property of RNA Thermometers Unique?

 

ABSTRACT A large number of studies have been dedicated to identify the structural and sequence based features of RNA thermometers, mRNAs that regulate their translation initiation rate with temperature. It has been shown that the melting of the ribosome-binding site (RBS) plays a prominent role in this thermosensing process. However, little is known as to … Continue readingResearch Summary: Is Thermosensing Property of RNA Thermometers Unique?

Research Summary: Exploring Small RNA Function

 

Abstract ____________________________ Publisher: Public Library of Science Author(s): Link: https://doi.org/10.1371/journal.pbio.0020114

Research Summary: Small Regulatory RNAs May Sharpen Spatial Expression Patterns

 

Abstract The precise establishment of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low spatial expression domains requires a genetic mechanism that exhibits sensitivity, yet is robust to fluctuations, a demand that may not be easily achieved by morphogens alone. Recently, it has been demonstrated that … Continue readingResearch Summary: Small Regulatory RNAs May Sharpen Spatial Expression Patterns

Research Summary: Association of the Long Non-coding RNA Steroid Receptor RNA Activator (SRA) with TrxG and PRC2 Complexes

 

ABSTRACT Long non-coding RNAs (lncRNAs) have been recognized as key players in transcriptional regulation. We show that the lncRNA steroid receptor RNA activator (SRA) participates in regulation through complex formation with trithorax group (TrxG) and polycomb repressive complex 2 (PRC2) complexes. Binding of the SRA-associated RNA helicase p68 preferentially stabilizes complex formation between SRA and … Continue readingResearch Summary: Association of the Long Non-coding RNA Steroid Receptor RNA Activator (SRA) with TrxG and PRC2 Complexes

Research Summary: Transposable-Element Associated Small RNAs in Bombyx mori Genome

 

ABSTRACT Small RNAs are a group of regulatory RNA molecules that control gene expression at transcriptional or post-transcriptional levels among eukaryotes. The silkworm, Bombyx mori L., genome harbors abundant repetitive sequences derived from families of retrotransposons and transposons, which together constitute almost half of the genome space and provide ample resource for biogenesis of the … Continue readingResearch Summary: Transposable-Element Associated Small RNAs in Bombyx mori Genome

Research Summary: RNA Processing Factors Swd2.2 and Sen1 Antagonize RNA Pol III-Dependent Transcription and the Localization of Condensin at Pol III Genes

 

ABSTRACT Condensin-mediated chromosome condensation is essential for genome stability upon cell division. Genetic studies have indicated that the association of condensin with chromatin is intimately linked to gene transcription, but what transcription-associated feature(s) direct(s) the accumulation of condensin remains unclear. Here we show in fission yeast that condensin becomes strikingly enriched at RNA Pol III-transcribed … Continue readingResearch Summary: RNA Processing Factors Swd2.2 and Sen1 Antagonize RNA Pol III-Dependent Transcription and the Localization of Condensin at Pol III Genes

Research Summary: Characterization of Unique Small RNA Populations from Rice Grain

 

ABSTRACT Small RNAs (∼20 to 24 nucleotides) function as naturally occurring molecules critical in developmental pathways in plants and animals [1], [2]. Here we analyze small RNA populations from mature rice grain and seedlings by pyrosequencing. Using a clustering algorithm to locate regions producing small RNAs, we classified hotspots of small RNA generation within the … Continue readingResearch Summary: Characterization of Unique Small RNA Populations from Rice Grain

Research Summary: Protein Solubility and Folding Enhancement by Interaction with RNA

 

ABSTRACT While basic mechanisms of several major molecular chaperones are well understood, this machinery has been known to be involved in folding of only limited number of proteins inside the cells. Here, we report a chaperone type of protein folding facilitated by interaction with RNA. When an RNA-binding module is placed at the N-terminus of … Continue readingResearch Summary: Protein Solubility and Folding Enhancement by Interaction with RNA

Research Summary: Deep Sequencing of RNA from Ancient Maize Kernels

 

ABSTRACT The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited – perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for long-term RNA survival, … Continue readingResearch Summary: Deep Sequencing of RNA from Ancient Maize Kernels

Research Summary: Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction

 

ABSTRACT Background Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation of viroid-derived 21–24 nt small RNAs (vd-sRNAs) with the typical features of the small interfering RNAs characteristic of … Continue readingResearch Summary: Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction

Research Summary: Small RNAs Originated from Pseudogenes: cis– or trans-Acting?

 

Abstract Pseudogenes are significant components of eukaryotic genomes, and some have acquired novel regulatory roles. To date, no study has characterized rice pseudogenes systematically or addressed their impact on the structure and function of the rice genome. In this genome-wide study, we have identified 11,956 non-transposon-related rice pseudogenes, most of which are from gene duplications. … Continue readingResearch Summary: Small RNAs Originated from Pseudogenes: cis– or trans-Acting?

Research Summary: Henipavirus RNA in African Bats

 

ABSTRACT Background Henipaviruses (Hendra and Nipah virus) are highly pathogenic members of the family Paramyxoviridae. Fruit-eating bats of the Pteropus genus have been suggested as their natural reservoir. Human Henipavirus infections have been reported in a region extending from Australia via Malaysia into Bangladesh, compatible with the geographic range of Pteropus. These bats do not … Continue readingResearch Summary: Henipavirus RNA in African Bats

Research Summary: Global Analyses of Small Interfering RNAs Derived from Bamboo mosaic virus and Its Associated Satellite RNAs in Different Plants

 

ABSTRACT Background Satellite RNAs (satRNAs), virus parasites, are exclusively associated with plant virus infection and have attracted much interest over the last 3 decades. Upon virus infection, virus-specific small interfering RNAs (vsiRNAs) are produced by dicer-like (DCL) endoribonucleases for anti-viral defense. The composition of vsiRNAs has been studied extensively; however, studies of satRNA-derived siRNAs (satsiRNAs) … Continue readingResearch Summary: Global Analyses of Small Interfering RNAs Derived from Bamboo mosaic virus and Its Associated Satellite RNAs in Different Plants

Research Summary: Hepatitis C Virus Translation Preferentially Depends on Active RNA Replication

 

ABSTRACT Hepatitis C virus (HCV) RNA initiates its replication on a detergent-resistant membrane structure derived from the endoplasmic reticulum (ER) in the HCV replicon cells. By performing a pulse-chase study of BrU-labeled HCV RNA, we found that the newly-synthesized HCV RNA traveled along the anterograde-membrane traffic and moved away from the ER. Presumably, the RNA … Continue readingResearch Summary: Hepatitis C Virus Translation Preferentially Depends on Active RNA Replication

Research Summary: Structure Prediction of RNA Loops with a Probabilistic Approach

 

Abstract The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical … Continue readingResearch Summary: Structure Prediction of RNA Loops with a Probabilistic Approach

Research Summary: Mammalian Small Nucleolar RNAs Are Mobile Genetic Elements

 

Abstract Small nucleolar RNAs (snoRNAs) of the H/ACA box and C/D box categories guide the pseudouridylation and the 2′-O-ribose methylation of ribosomal RNAs by forming short duplexes with their target. Similarly, small Cajal body–specific RNAs (scaRNAs) guide modifications of spliceosomal RNAs. The vast majority of vertebrate sno/scaRNAs are located in introns of genes transcribed by … Continue readingResearch Summary: Mammalian Small Nucleolar RNAs Are Mobile Genetic Elements

Research Summary: Xist RNA in action: Past, present, and future

 

ABSTRACT In mammals, dosage compensation of sex chromosomal genes between females (XX) and males (XY) is achieved through X-chromosome inactivation (XCI). The X-linked X-inactive-specific transcript (Xist) long noncoding RNA is indispensable for XCI and initiates the process early during development by spreading in cis across the X chromosome from which it is transcribed. During XCI, … Continue readingResearch Summary: Xist RNA in action: Past, present, and future

Research Summary: A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: De Novo Detection in Human Spinal Cord Tissue

 

ABSTRACT RNA editing is a post-transcriptional process occurring in a wide range of organisms. In human brain, the A-to-I RNA editing, in which individual adenosine (A) bases in pre-mRNA are modified to yield inosine (I), is the most frequent event. Modulating gene expression, RNA editing is essential for cellular homeostasis. Indeed, its deregulation has been … Continue readingResearch Summary: A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: De Novo Detection in Human Spinal Cord Tissue

Research Summary: Efficient Algorithms for Probing the RNA Mutation Landscape

 

Abstract The diversity and importance of the role played by RNAs in the regulation and development of the cell are now well-known and well-documented. This broad range of functions is achieved through specific structures that have been (presumably) optimized through evolution. State-of-the-art methods, such as McCaskill’s algorithm, use a statistical mechanics framework based on the … Continue readingResearch Summary: Efficient Algorithms for Probing the RNA Mutation Landscape

Research Summary: RNA–Mediated Epigenetic Heredity Requires the Cytosine Methyltransferase Dnmt2

 

Abstract RNA–mediated transmission of phenotypes is an important way to explain non-Mendelian heredity. We have previously shown that small non-coding RNAs can induce hereditary epigenetic variations in mice and act as the transgenerational signalling molecules. Two prominent examples for these paramutations include the epigenetic modulation of the Kit gene, resulting in altered fur coloration, and … Continue readingResearch Summary: RNA–Mediated Epigenetic Heredity Requires the Cytosine Methyltransferase Dnmt2

Research Summary: Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

 

Abstract The assumption that RNA can be readily classified into either protein-coding or non-protein–coding categories has pervaded biology for close to 50 years. Until recently, discrimination between these two categories was relatively straightforward: most transcripts were clearly identifiable as protein-coding messenger RNAs (mRNAs), and readily distinguished from the small number of well-characterized non-protein–coding RNAs (ncRNAs), … Continue readingResearch Summary: Differentiating Protein-Coding and Noncoding RNA: Challenges and
Ambiguities

Research Summary: UPF201 Archaeal Specific Family Members Reveal Structural Similarity to RNA-Binding Proteins but Low Likelihood for RNA-Binding Function

 

ABSTRACT We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54) to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10–40%) and the absence of conserved sequence motifs, the three-dimensional structures of these proteins … Continue readingResearch Summary: UPF201 Archaeal Specific Family Members Reveal Structural Similarity to RNA-Binding Proteins but Low Likelihood for RNA-Binding Function

Research Summary: Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

 

ABSTRACT The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA … Continue readingResearch Summary: Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

Research Summary: The Genetic Signatures of Noncoding RNAs

 

Abstract The majority of the genome in animals and plants is transcribed in a developmentally regulated manner to produce large numbers of non–protein-coding RNAs (ncRNAs), whose incidence increases with developmental complexity. There is growing evidence that these transcripts are functional, particularly in the regulation of epigenetic processes, leading to the suggestion that they compose a … Continue readingResearch Summary: The Genetic Signatures of Noncoding RNAs

Research Summary: Ubiquitous Expression of CUG or CAG Trinucleotide Repeat RNA Causes Common Morphological Defects in a Drosophila Model of RNA-Mediated Pathology

 

ABSTRACT Expanded DNA repeat sequences are known to cause over 20 diseases, including Huntington’s disease, several types of spinocerebellar ataxia and myotonic dystrophy type 1 and 2. A shared genetic basis, and overlapping clinical features for some of these diseases, indicate that common pathways may contribute to pathology. Multiple mechanisms, mediated by both expanded homopolymeric … Continue readingResearch Summary: Ubiquitous Expression of CUG or CAG Trinucleotide Repeat RNA Causes Common Morphological Defects in a Drosophila Model of RNA-Mediated Pathology

Research Summary: Query-Dependent Banding (QDB) for Faster RNA Similarity Searches

 

Abstract When searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity. Covariance models (CMs) are probabilistic models well-suited for RNA similarity search applications. However, the computational complexity of CM dynamic programming alignment algorithms has limited their practical application. Here we describe an acceleration method called query-dependent … Continue readingResearch Summary: Query-Dependent Banding (QDB) for Faster RNA Similarity Searches

Research Summary: Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction

 

Abstract Predicting RNA-binding protein (RBP) specificity is important for understanding gene expression regulation and RNA-mediated enzymatic processes. It is widely believed that RBP binding specificity is determined by both the sequence and structural contexts of RNAs. Existing approaches, including traditional machine learning algorithms and more recently, deep learning models, have been extensively applied to integrate … Continue readingResearch Summary: Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction

Research Summary: Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs

 

Abstract RNA molecules will tend to adopt a folded conformation through the pairing of bases on a single strand; the resulting so-called secondary structure is critical to the function of many types of RNA. The secondary structure of a particular substring of functional RNA may depend on its surrounding sequence. Yet, some RNAs such as … Continue readingResearch Summary: Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs

Research Summary: Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines

 

Abstract An increasing number of cis-regulatory RNA elements have been found to regulate gene expression post-transcriptionally in various biological processes in bacterial systems. Effective computational tools for large-scale identification of novel regulatory RNAs are strongly desired to facilitate our exploration of gene regulation mechanisms and regulatory networks. We present a new computational program named RSSVM … Continue readingResearch Summary: Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines

Research Summary: The Efficacy of Generating Three Independent Anti-HIV-1 siRNAs from a Single U6 RNA Pol III-Expressed Long Hairpin RNA

 

ABSTRACT RNA Interference (RNAi) effectors have been used to inhibit rogue RNAs in mammalian cells. However, rapidly evolving sequences such as the human immunodeficiency virus type 1 (HIV-1) require multiple targeting approaches to prevent the emergence of escape variants. Expressed long hairpin RNAs (lhRNAs) have recently been used as a strategy to produce multiple short … Continue readingResearch Summary: The Efficacy of Generating Three Independent Anti-HIV-1 siRNAs from a Single U6 RNA Pol III-Expressed Long Hairpin RNA

Research Summary: The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum

 

ABSTRACT Background The mitochondrial genome in the human malaria parasite Plasmodium falciparum is most unusual. Over half the genome is composed of the genes for three classic mitochondrial proteins: cytochrome oxidase subunits I and III and apocytochrome b. The remainder encodes numerous small RNAs, ranging in size from 23 to 190 nt. Previous analysis revealed … Continue readingResearch Summary: The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum

Research Summary: Focal Distribution of Hepatitis C Virus RNA in Infected Livers

 

ABSTRACT Background Hepatitis C virus (HCV) is a plus-strand RNA virus that replicates by amplification of genomic RNA from minus strands leading to accumulation of almost one thousand copies per cell under in vitro cell culture conditions. In contrast, HCV RNA copy numbers in livers of infected patients appear to be much lower, estimated at … Continue readingResearch Summary: Focal Distribution of Hepatitis C Virus RNA in Infected Livers

Research Summary: Structural Constraints Identified with Covariation Analysis in Ribosomal RNA

 

ABSTRACT Covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of RNA sequences. These constraints on the evolution of two positions are usually associated with a base pair in a helix. While mutual information (MI) has been used to accurately predict an RNA secondary structure and a … Continue readingResearch Summary: Structural Constraints Identified with Covariation Analysis in Ribosomal RNA

Research Summary: Evolution of Mutational Robustness in an RNA Virus

 

Abstract Mutational (genetic) robustness is phenotypic constancy in the face of mutational changes to the genome. Robustness is critical to the understanding of evolution because phenotypically expressed genetic variation is the fuel of natural selection. Nonetheless, the evidence for adaptive evolution of mutational robustness in biological populations is controversial. Robustness should be selectively favored when … Continue readingResearch Summary: Evolution of Mutational Robustness in an RNA Virus

Research Summary: RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

 

Abstract Microsatellite expansions cause a number of dominantly-inherited neurological diseases. Expansions in coding-regions cause protein gain-of-function effects, while non-coding expansions produce toxic RNAs that alter RNA splicing activities of MBNL and CELF proteins. Bi-directional expression of the spinocerebellar ataxia type 8 (SCA8) CTG CAG expansion produces CUG expansion RNAs (CUGexp) from the ATXN8OS gene and … Continue readingResearch Summary: RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

Research Summary: Comparative Structural Analysis of Human DEAD-Box RNA Helicases

 

ABSTRACT DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these … Continue readingResearch Summary: Comparative Structural Analysis of Human DEAD-Box RNA Helicases

Research Summary: MLN51 Stimulates the RNA-Helicase Activity of eIF4AIII

 

ABSTRACT The core of the exon-junction complex consists of Y14, Magoh, MLN51 and eIF4AIII, a DEAD-box RNA helicase. MLN51 stimulates the ATPase activity of eIF4AIII, whilst the Y14-Magoh complex inhibits it. We show that the MLN51-dependent stimulation increases both the affinity of eIF4AIII for ATP and the rate of enzyme turnover; the KM is decreased … Continue readingResearch Summary: MLN51 Stimulates the RNA-Helicase Activity of eIF4AIII

Research Summary: Trans-kingdom Cross-Talk: Small RNAs on the Move

 

ABSTRACT This review focuses on the mobility of small RNA (sRNA) molecules from the perspective of trans-kingdom gene silencing. Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years … Continue readingResearch Summary: Trans-kingdom Cross-Talk: Small RNAs on the Move

Research Summary: Pseudo–Messenger RNA: Phantoms of the Transcriptome

 

Abstract The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo–messenger RNA to be RNA molecules that resemble protein-coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo–messenger RNAs … Continue readingResearch Summary: Pseudo–Messenger RNA: Phantoms of the Transcriptome

Research Summary: RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

 

ABSTRACT Genome-wide expression analysis using next generation sequencing (RNA-Seq) provides an opportunity for in-depth molecular profiling of fundamental biological processes, such as cellular differentiation and malignant transformation. Differentiating human neurons derived from induced pluripotent stem cells (iPSCs) provide an ideal system for RNA-Seq since defective neurogenesis caused by abnormalities in transcription factors, DNA methylation, and … Continue readingResearch Summary: RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

Research Summary: The Structure of an RNAi Polymerase Links RNA Silencing and Transcription

 

Abstract RNA silencing refers to a group of RNA-induced gene-silencing mechanisms that developed early in the eukaryotic lineage, probably for defence against pathogens and regulation of gene expression. In plants, protozoa, fungi, and nematodes, but apparently not insects and vertebrates, it involves a cell-encoded RNA-dependent RNA polymerase (cRdRP) that produces double-stranded RNA triggers from aberrant … Continue readingResearch Summary: The Structure of an RNAi Polymerase Links RNA Silencing and Transcription

Research Summary: Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana

 

ABSTRACT This study presents the first characterization of endogenous small RNAs in a diatom, Thalassiosira pseudonana. Small RNAs act as transcriptional and translational regulators, controlling specific target genes involved in various cellular functions. Diatoms are unicellular photosynthetic organisms that play major roles in environmental processes, such as food webs and global carbon fixation. Small RNA … Continue readingResearch Summary: Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana

Research Summary: Conformational Features of Topologically Classified RNA Secondary Structures

 

ABSTRACT Background Current RNA secondary structure prediction approaches predict prevalent pseudoknots such as the H-pseudoknot and kissing hairpin. The number of possible structures increases drastically when more complex pseudoknots are considered, thus leading to computational limitations. On the other hand, the enormous population of possible structures means not all of them appear in real RNA … Continue readingResearch Summary: Conformational Features of Topologically Classified RNA Secondary Structures

Research Summary: RNA Unwinding by NS3 Helicase: A Statistical Approach

 

ABSTRACT The study of double-stranded RNA unwinding by helicases is a problem of basic scientific interest. One such example is provided by studies on the hepatitis C virus (HCV) NS3 helicase using single molecule mechanical experiments. HCV currently infects nearly 3% of the world population and NS3 is a protein essential for viral genome replication. … Continue readingResearch Summary: RNA Unwinding by NS3 Helicase: A Statistical Approach

Research Summary: Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

 

Abstract Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral. We report herein that high-throughput chemical experiments can isolate an RNA’s multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2) and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states’ … Continue readingResearch Summary: Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

Research Summary: Repetitive Editing and RNA Splicing

 

Abstract ____________________________ Publisher: Public Library of Science Author(s): Link: https://doi.org/10.1371/journal.pbio.0020426

Research Summary: More GC Means More RNA

 

Abstract ____________________________ Publisher: Public Library of Science Author(s): Robinson R. Link: https://doi.org/10.1371/journal.pbio.0040206

Research Summary: Small RNA Pathways in Plants

 

Abstract ____________________________ Publisher: Public Library of Science Author(s): Link: https://doi.org/10.1371/journal.pbio.0020107

Research Summary: Genetic and Functional Diversification of Small RNA Pathways in Plants

 

Abstract Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that … Continue readingResearch Summary: Genetic and Functional Diversification of Small RNA Pathways in Plants

Research Summary: Nondenaturing Purification of Co-Transcriptionally Folded RNA Avoids Common Folding Heterogeneity

 

ABSTRACT Due to the energetic frustration of RNA folding, tertiary structured RNA is typically characterized by a rugged folding free energy landscape where deep kinetic barriers separate numerous misfolded states from one or more native states. While most in vitro studies of RNA rely on (re)folding chemically and/or enzymatically synthesized RNA in its entirety, which … Continue readingResearch Summary: Nondenaturing Purification of Co-Transcriptionally Folded RNA Avoids Common Folding Heterogeneity

Research Summary: The evolution and adaptation of A-to-I RNA editing

 

ABSTRACT Adenosine-to-inosine (A-to-I) RNA editing is an important post-transcriptional modification that affects the information encoded from DNA to RNA to protein. RNA editing can generate a multitude of transcript isoforms and can potentially be used to optimize protein function in response to varying conditions. In light of this and the fact that millions of editing … Continue readingResearch Summary: The evolution and adaptation of A-to-I RNA editing

Research Summary: Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

 

ABSTRACT Short non-coding transcripts can be transcribed from distant-acting transcriptional enhancer loci, but the prevalence of such enhancer RNAs (eRNAs) within the transcriptome, and the association of eRNA expression with tissue-specific enhancer activity in vivo remain poorly understood. Here, we investigated the expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues via deep RNA … Continue readingResearch Summary: Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

Research Summary: The small RNA complement of adult Schistosoma haematobium

 

ABSTRACT Background Blood flukes of the genus Schistosoma cause schistosomiasis—a neglected tropical disease (NTD) that affects more than 200 million people worldwide. Studies of schistosome genomes have improved our understanding of the molecular biology of flatworms, but most of them have focused largely on protein-coding genes. Small non-coding RNAs (sncRNAs) have been explored in selected … Continue readingResearch Summary: The small RNA complement of adult Schistosoma haematobium

Research Summary: Autoregulation of the Drosophila Noncoding roX1 RNA Gene

 

Abstract Most genes along the male single X chromosome in Drosophila are hypertranscribed about two-fold relative to each of the two female X chromosomes. This is accomplished by the MSL (male-specific lethal) complex that acetylates histone H4 at lysine 16. The MSL complex contains two large noncoding RNAs, roX1 (RNA on X) and roX2, that … Continue readingResearch Summary: Autoregulation of the Drosophila Noncoding roX1 RNA Gene

Research Summary: Innate Immune Suppression Enables Frequent Transfection with RNA Encoding Reprogramming Proteins

 

ABSTRACT Background Generating autologous pluripotent stem cells for therapeutic applications will require the development of efficient DNA-free reprogramming techniques. Transfecting cells with in vitro-transcribed, protein-encoding RNA is a straightforward method of directly expressing high levels of reprogramming proteins without genetic modification. However, long-RNA transfection triggers a potent innate immune response characterized by growth inhibition and … Continue readingResearch Summary: Innate Immune Suppression Enables Frequent Transfection with RNA Encoding Reprogramming Proteins

Research Summary: Nuclear Outsourcing of RNA Interference Components to Human Mitochondria

 

ABSTRACT MicroRNAs (miRNAs) are small non-coding RNAs that associate with Argonaute proteins to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in other cellular compartments. Mitochondria harbour their own genetic system that may be a potential site for miRNA mediated post-transcriptional … Continue readingResearch Summary: Nuclear Outsourcing of RNA Interference Components to Human Mitochondria

Research Summary: RNA Editome in Rhesus Macaque Shaped by Purifying Selection

 

Abstract Understanding of the RNA editing process has been broadened considerably by the next generation sequencing technology; however, several issues regarding this regulatory step remain unresolved – the strategies to accurately delineate the editome, the mechanism by which its profile is maintained, and its evolutionary and functional relevance. Here we report an accurate and quantitative … Continue readingResearch Summary: RNA Editome in Rhesus Macaque Shaped by Purifying Selection

Research Summary: Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling

 

Abstract Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. The emergence of new technologies for … Continue readingResearch Summary: Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling

Research Summary: Evidence for Large Complex Networks of Plant Short Silencing RNAs

 

ABSTRACT Background In plants and animals there are many classes of short RNAs that carry out a wide range of functions within the cell; short silencing RNAs (ssRNAs) of 21–25 nucleotides in length are produced from double-stranded RNA precursors by the protein Dicer and guide nucleases and other proteins to their RNA targets through base … Continue readingResearch Summary: Evidence for Large Complex Networks of Plant Short Silencing RNAs

Research Summary: Evidence for Large Complex Networks of Plant Short Silencing RNAs

 

ABSTRACT Background In plants and animals there are many classes of short RNAs that carry out a wide range of functions within the cell; short silencing RNAs (ssRNAs) of 21–25 nucleotides in length are produced from double-stranded RNA precursors by the protein Dicer and guide nucleases and other proteins to their RNA targets through base … Continue readingResearch Summary: Evidence for Large Complex Networks of Plant Short Silencing RNAs

Research Summary: Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae

 

ABSTRACT The vast landscape of RNA-protein interactions at the heart of post-transcriptional regulation remains largely unexplored. Indeed it is likely that, even in yeast, a substantial fraction of the regulatory RNA-binding proteins (RBPs) remain to be discovered. Systematic experimental methods can play a key role in discovering these RBPs – most of the known yeast … Continue readingResearch Summary: Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae

Research Summary: Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

 

Abstract Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches), a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the function of an RNA, we expect to observe evolutionary co-variation supporting multiple conformations. … Continue readingResearch Summary: Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

Research Summary: Evidence for an RNA Polymerization Activity in Axolotl and Xenopus Egg Extracts

 

ABSTRACT We have previously reported a post-transcriptional RNA amplification observed in vivo following injection of in vitro synthesized transcripts into axolotl oocytes, unfertilized (UFE) or fertilized eggs. To further characterize this phenomenon, low speed extracts (LSE) from axolotl and Xenopus UFE were prepared and tested in an RNA polymerization assay. The major conclusions are: i) … Continue readingResearch Summary: Evidence for an RNA Polymerization Activity in Axolotl and Xenopus Egg Extracts

Research Summary: abd-A Regulation by the iab-8 Noncoding RNA

 

Abstract The homeotic genes in Drosophila melanogaster are aligned on the chromosome in the order of the body segments that they affect. The genes affecting the more posterior segments repress the more anterior genes. This posterior dominance rule must be qualified in the case of abdominal-A (abd-A) repression by Abdominal-B (Abd-B). Animals lacking Abd-B show … Continue readingResearch Summary: abd-A Regulation by the iab-8 Noncoding RNA

Research Summary: Modulating the Expression of Disease Genes with RNA-Based Therapy

 

Abstract Conventional gene therapy has focused largely on gene replacement in target cells. However, progress from basic research to the clinic has been slow for reasons relating principally to the challenges of heterologous DNA delivery and regulation in vivo. Alternative approaches targeting RNA have the potential to circumvent some of these difficulties, particularly as the … Continue readingResearch Summary: Modulating the Expression of Disease Genes with RNA-Based Therapy

Research Summary: Less Can Be More: RNA-Adapters May Enhance Coding Capacity of Replicators

 

ABSTRACT It is still not clear how prebiotic replicators evolved towards the complexity found in present day organisms. Within the most realistic scenario for prebiotic evolution, known as the RNA world hypothesis, such complexity has arisen from replicators consisting solely of RNA. Within contemporary life, remarkably many RNAs are involved in modifying other RNAs. In … Continue readingResearch Summary: Less Can Be More: RNA-Adapters May Enhance Coding Capacity of Replicators

Research Summary: New Perspectives on DNA and RNA Triplexes As Effectors of Biological Activity

 

ABSTRACT Since the first description of the canonical B-form DNA double helix, it has been suggested that alternative DNA, DNA–RNA, and RNA structures exist and act as functional genomic elements. Indeed, over the past few years it has become clear that, in addition to serving as a repository for genetic information, genomic DNA elicits biological … Continue readingResearch Summary: New Perspectives on DNA and RNA Triplexes As Effectors of Biological Activity

Research Summary: Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism

 

Abstract Trf4p and Trf5p are non-canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short-lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of … Continue readingResearch Summary: Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism

Research Summary: Subversion of Cellular Autophagosomal Machinery by RNA Viruses

 

Abstract Infection of human cells with poliovirus induces the proliferation of double-membraned cytoplasmic vesicles whose surfaces are used as the sites of viral RNA replication and whose origin is unknown. Here, we show that several hallmarks of cellular autophagosomes can be identified in poliovirus-induced vesicles, including colocalization of LAMP1 and LC3, the human homolog of … Continue readingResearch Summary: Subversion of Cellular Autophagosomal Machinery by RNA Viruses

Research Summary: The Role of Human Dicer-dsRBD in Processing Small Regulatory RNAs

 

ABSTRACT One of the most exciting recent developments in RNA biology has been the discovery of small non-coding RNAs that affect gene expression through the RNA interference (RNAi) mechanism. Two major classes of RNAs involved in RNAi are small interfering RNA (siRNA) and microRNA (miRNA). Dicer, an RNase III enzyme, plays a central role in … Continue readingResearch Summary: The Role of Human Dicer-dsRBD in Processing Small Regulatory RNAs

Research Summary: Selective Pharmacological Targeting of a DEAD Box RNA Helicase

 

ABSTRACT RNA helicases represent a large family of proteins implicated in many biological processes including ribosome biogenesis, splicing, translation and mRNA degradation. However, these proteins have little substrate specificity, making inhibition of selected helicases a challenging problem. The prototypical DEAD box RNA helicase, eIF4A, works in conjunction with other translation factors to prepare mRNA templates … Continue readingResearch Summary: Selective Pharmacological Targeting of a DEAD Box RNA Helicase

Research Summary: Correction: Nicotiana Small RNA Sequences Support a Host Genome Origin of Cucumber Mosaic Virus Satellite RNA

 

Partial Text This article was republished on April 2nd, 2015, to correct errors in the footer year, the citation year and copyright year that were introduced during the typesetting process. The publisher apologizes for the errors. Please download this article again to view the correct version. The originally published, uncorrected article and the republished, corrected … Continue readingResearch Summary: Correction: Nicotiana Small RNA Sequences Support a Host Genome Origin of Cucumber Mosaic Virus Satellite RNA

Research Summary: Correction: Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson’s Leukocytes Identified by RNA Sequencing

 

Abstract ____________________________ Publisher: Public Library of Science Date Published: 16-May-2014 Author(s): Soreq L. Link: https://doi.org/10.1371/journal.pcbi.1003647

Research Summary: From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

 

Abstract Non-coding RNAs (ncRNAs) are receiving more and more attention not only as an abundant class of genes, but also as regulatory structural elements (some located in mRNAs). A key feature of RNA function is its structure. Computational methods were developed early for folding and prediction of RNA structure with the aim of assisting in … Continue readingResearch Summary: From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

Research Summary: Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life

 

Abstract The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between the earliest stages in the evolution of life and the RNA repertoires of extant lineages. Some … Continue readingResearch Summary: Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life

Research Summary: Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

 

Abstract The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human genome and used it to survey an eight-way … Continue readingResearch Summary: Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

Research Summary: On the optimal design of metabolic RNA labeling experiments

 

Abstract Massively parallel RNA sequencing (RNA-seq) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription, processing or decay. Regardless of advances in the experimental protocols and techniques, every experimentalist needs to specify the key aspects of experimental design: For example, which protocol should be used (biochemical … Continue readingResearch Summary: On the optimal design of metabolic RNA labeling experiments

Research Summary: Inhibitors of Foot and Mouth Disease Virus Targeting a Novel Pocket of the RNA-Dependent RNA Polymerase

 

ABSTRACT Background Foot-and-Mouth Disease Virus (FMDV) is a picornavirus that infects cloven-hoofed animals and leads to severe losses in livestock production. In the case of an FMD outbreak, emergency vaccination requires at least 7 days to trigger an effective immune response. There are currently no approved inhibitors for the treatment or prevention of FMDV infections. … Continue readingResearch Summary: Inhibitors of Foot and Mouth Disease Virus Targeting a Novel Pocket of the RNA-Dependent RNA Polymerase

Research Summary: Gadd45a Is an RNA Binding Protein and Is Localized in Nuclear Speckles

 

ABSTRACT Background The Gadd45 proteins play important roles in growth control, maintenance of genomic stability, DNA repair, and apoptosis. Recently, Gadd45 proteins have also been implicated in epigenetic gene regulation by promoting active DNA demethylation. Gadd45 proteins have sequence homology with the L7Ae/L30e/S12e RNA binding superfamily of ribosomal proteins, which raises the question if they … Continue readingResearch Summary: Gadd45a Is an RNA Binding Protein and Is Localized in Nuclear Speckles

Research Summary: Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

 

Abstract Abstract Deciphering how the regulatory DNA sequence of a gene dictates its expression in response to intra and extracellular cues is one of the leading challenges in modern genomics. The development of novel single-cell sequencing and imaging techniques, as well as a better exploitation of currently available single-molecule imaging techniques, provides an avenue to … Continue readingResearch Summary: Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

Research Summary: Complementarity of End Regions Increases the Lifetime of Small RNAs in Mammalian Cells

 

ABSTRACT Two RNAs (4.5SH and 4.5SI) with unknown functions share a number of features: short length (about 100 nt), transcription by RNA polymerase III, predominately nuclear localization, the presence in various tissues, and relatively narrow taxonomic distribution (4 and 3 rodent families, respectively). It was reported that 4.5SH RNA turns over rapidly, whereas 4.5SI RNA … Continue readingResearch Summary: Complementarity of End Regions Increases the Lifetime of Small RNAs in Mammalian Cells

Research Summary: Cytoplasmic CUG RNA Foci Are Insufficient to Elicit Key DM1 Features

 

ABSTRACT The genetic basis of myotonic dystrophy type I (DM1) is the expansion of a CTG tract located in the 3′ untranslated region of DMPK. Expression of mutant RNAs encoding expanded CUG repeats plays a central role in the development of cardiac disease in DM1. Expanded CUG tracts form both nuclear and cytoplasmic aggregates, yet … Continue readingResearch Summary: Cytoplasmic CUG RNA Foci Are Insufficient to Elicit Key DM1 Features

Research Abstract: Evolution of RNA-Protein Interactions: Non-Specific Binding Led to RNA Splicing Activity of Fungal Mitochondrial Tyrosyl-tRNA Synthetases

 

Abstract Studies of tRNA synthetases that adapted to assist the splicing of group I introns provide insight into how proteins can evolve new RNA-binding functions. ____________________________ Publisher: Public Library of Science Date Published: 23-December-2014 Author(s): Lamech L., Mallam A., Lambowitz A. Link: https://doi.org/10.1371/journal.pbio.1002028

Research Summary: Disease-Associated Mutations That Alter the RNA Structural Ensemble

 

Abstract Genome-wide association studies (GWAS) often identify disease-associated mutations in intergenic and non-coding regions of the genome. Given the high percentage of the human genome that is transcribed, we postulate that for some observed associations the disease phenotype is caused by a structural rearrangement in a regulatory region of the RNA transcript. To identify such … Continue readingResearch Summary: Disease-Associated Mutations That Alter the RNA Structural Ensemble

Research Summary: Cytosine-5 RNA methylation links protein synthesis to cell metabolism

 

Abstract Posttranscriptional modifications in transfer RNA (tRNA) are often critical for normal development because they adapt protein synthesis rates to a dynamically changing microenvironment. However, the precise cellular mechanisms linking the extrinsic stimulus to the intrinsic RNA modification pathways remain largely unclear. Here, we identified the cytosine-5 RNA methyltransferase NSUN2 as a sensor for external … Continue readingResearch Summary: Cytosine-5 RNA methylation links protein synthesis to cell metabolism

Research Summary: Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes

 

ABSTRACT Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP) assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, … Continue readingResearch Summary: Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes

Research Summary: The Human Nuclear Poly(A)-Binding Protein Promotes RNA Hyperadenylation and Decay

 

Abstract Control of nuclear RNA stability is essential for proper gene expression, but the mechanisms governing RNA degradation in mammalian nuclei are poorly defined. In this study, we uncover a mammalian RNA decay pathway that depends on the nuclear poly(A)-binding protein (PABPN1), the poly(A) polymerases (PAPs), PAPα and PAPγ, and the exosome subunits RRP6 and … Continue readingResearch Summary: The Human Nuclear Poly(A)-Binding Protein Promotes RNA Hyperadenylation and Decay

Research Summary: A Phagocytic Route for Uptake of Double-Stranded RNA in RNAi

 

ABSTRACT RNA interference (RNAi) has a range of physiological functions including as a defence mechanism against viruses. To protect uninfected cells in a multicellular organism, not only a cell-autonomous RNAi response is required but also a systemic one. However, the route of RNA spread in systemic RNAi remains unclear. Here we show that phagocytosis can … Continue readingResearch Summary: A Phagocytic Route for Uptake of Double-Stranded RNA in RNAi

Research Summary: Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

 

ABSTRACT An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally … Continue readingResearch Summary: Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

Research Summary: Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

 

Abstract Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, … Continue readingResearch Summary: Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

Research Summary: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus

 

ABSTRACT Annexin A2 (ANXA2) is a protein implicated in diverse cellular functions, including exocytosis, DNA synthesis and cell proliferation. It was recently proposed to be involved in RNA metabolism because it was shown to associate with some cellular mRNA. Here, we identified ANXA2 as a RNA binding protein (RBP) that binds IBV (Infectious Bronchitis Virus) … Continue readingResearch Summary: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus

Research Summary: Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins

 

Abstract Long noncoding RNAs constitute a major fraction of the eukaryotic transcriptome, and together with proteins, they intricately fine-tune various growth regulatory signals to control cellular homeostasis. Here, we describe the functional characterisation of a novel pair of long intergenic noncoding RNAs (lincRNAs) comprised of complementary, fully overlapping sense and antisense transcripts Genomic Instability Inducing … Continue readingResearch Summary: Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins

Research Summary: A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

 

Abstract The pentatricopeptide repeat (PPR) is a helical repeat motif found in an exceptionally large family of RNA–binding proteins that functions in mitochondrial and chloroplast gene expression. PPR proteins harbor between 2 and 30 repeats and typically bind single-stranded RNA in a sequence-specific fashion. However, the basis for sequence-specific RNA recognition by PPR tracts has … Continue readingResearch Summary: A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

Research Summary: Systematic Identification of Novel, Essential Host Genes Affecting Bromovirus RNA Replication

 

ABSTRACT Positive-strand RNA virus replication involves viral proteins and cellular proteins at nearly every replication step. Brome mosaic virus (BMV) is a well-established model for dissecting virus-host interactions and is one of very few viruses whose RNA replication, gene expression and encapsidation have been reproduced in the yeast Saccharomyces cerevisiae. Previously, our laboratory identified ∼100 … Continue readingResearch Summary: Systematic Identification of Novel, Essential Host Genes Affecting Bromovirus RNA Replication

Research Summary: The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome

 

Abstract We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all possess a motif at the 3′ end of their RNA genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation … Continue readingResearch Summary: The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome

Research Summary: Membrane Recognition and Dynamics of the RNA Degradosome

 

ABSTRACT RNase E, which is the central component of the multienzyme RNA degradosome, serves as a scaffold for interaction with other enzymes involved in mRNA degradation including the DEAD-box RNA helicase RhlB. Epifluorescence microscopy under live cell conditions shows that RNase E and RhlB are membrane associated, but neither protein forms cytoskeletal-like structures as reported … Continue readingResearch Summary: Membrane Recognition and Dynamics of the RNA Degradosome

Research Summary: Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding

 

ABSTRACT Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for … Continue readingResearch Summary: Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding

Research Summary: Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis

 

ABSTRACT Only few small RNAs (sRNAs) have been characterized in Mycobacterium tuberculosis and their role in regulatory networks is still poorly understood. Here we report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis of exponentially growing cultures of M. tuberculosis H37Rv had previously identified 1373 sRNA species. … Continue readingResearch Summary: Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis

Research Summary: Repression of RNA Polymerase II Transcription by a Drosophila Oligopeptide

 

ABSTRACT Background Germline progenitors resist signals that promote differentiation into somatic cells. This occurs through the transient repression in primordial germ cells of RNA polymerase II, specifically by disrupting Ser2 phosphorylation on its C-terminal domain. Methodology/Principal Findings Here we show that contrary to expectation the Drosophila polar granule component (pgc) gene functions as a protein … Continue readingResearch Summary: Repression of RNA Polymerase II Transcription by a Drosophila Oligopeptide

Research Summary: The RNA Silencing Pathway: The Bits and Pieces That Matter

 

Abstract Cellular pathways are generally proposed on the basis of available experimental knowledge. The proposed pathways, however, may be inadequate to describe the phenomena they are supposed to explain. For instance, by means of concise mathematical models we are able to reveal shortcomings in the current description of the pathway of RNA silencing. The silencing … Continue readingResearch Summary: The RNA Silencing Pathway: The Bits and Pieces That Matter

Research Summary: RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses

 

Abstract The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community present in healthy humans has not been described. Here, we present a comparative metagenomic analysis of the RNA viruses found in … Continue readingResearch Summary: RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses

Research Summary: SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

 

Abstract A major challenge in developmental biology is to understand the genetic and cellular processes/programs driving organ formation and differentiation of the diverse cell types that comprise the embryo. While recent studies using single cell transcriptome analysis illustrate the power to measure and understand cellular heterogeneity in complex biological systems, processing large amounts of RNA-seq … Continue readingResearch Summary: SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

Research Summary: Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

 

ABSTRACT Lariat RNAs formed as by-products of splicing are quickly degraded by the RNA debranching enzyme 1 (DBR1), leading to their turnover. Null dbr1 mutants in both animals and plants are embryo lethal, but the mechanism underlying the lethality remains unclear. Here we characterized a weak mutant allele of DBR1 in Arabidopsis, dbr1-2, and showed … Continue readingResearch Summary: Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

Research Summary: Impact of Collection Method on Assessment of Semen HIV RNA Viral Load

 

ABSTRACT Background The blood HIV RNA viral load is the best-defined predictor of HIV transmission, in part due to ease of measurement and the correlation of blood and genital tract (semen or cervico-vaginal) viral load, although recent studies found semen HIV RNA concentration to be a stronger predictor of HIV transmission. There is currently no … Continue readingResearch Summary: Impact of Collection Method on Assessment of Semen HIV RNA Viral Load

Research Summary: Two Seemingly Homologous Noncoding RNAs Act Hierarchically to Activate glmS mRNA Translation

 

Abstract Small noncoding RNAs (sRNA) can function as posttranscriptional activators of gene expression to regulate stress responses and metabolism. We here describe the mechanisms by which two sRNAs, GlmY and GlmZ, activate the Escherichia coli glmS mRNA, coding for an essential enzyme in amino-sugar metabolism. The two sRNAs, although being highly similar in sequence and … Continue readingResearch Summary: Two Seemingly Homologous Noncoding RNAs Act Hierarchically to Activate glmS mRNA Translation

Research Summary: Long-range control of gene expression via RNA-directed DNA methylation

 

ABSTRACT RNA-mediated transcriptional silencing, in plants known as RNA-directed DNA methylation (RdDM), is a conserved process where small interfering RNA (siRNA) and long non-coding RNA (lncRNA) help establish repressive chromatin modifications. This process represses transposons and affects the expression of protein-coding genes. We found that in Arabidopsis thaliana AGO4 binding sites are often located distant … Continue readingResearch Summary: Long-range control of gene expression via RNA-directed DNA methylation

Research Summary: Sequence Coevolution between RNA and Protein Characterized by Mutual Information between Residue Triplets

 

ABSTRACT Coevolving residues in a multiple sequence alignment provide evolutionary clues of biophysical interactions in 3D structure. Despite a rich literature describing amino acid coevolution within or between proteins and nucleic acid coevolution within RNA, to date there has been no direct evidence of coevolution between protein and RNA. The ribosome, a structurally conserved macromolecular … Continue readingResearch Summary: Sequence Coevolution between RNA and Protein Characterized by Mutual Information between Residue Triplets

Research Summary: Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA

 

Abstract Alternative cleavage and polyadenylation influence the coding and regulatory potential of mRNAs and where transcription termination occurs. Although widespread, few regulators of this process are known. The Arabidopsis thaliana protein FPA is a rare example of a trans-acting regulator of poly(A) site choice. Analysing fpa mutants therefore provides an opportunity to reveal generic consequences … Continue readingResearch Summary: Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA

Research Summary: Two-Step Recruitment of RNA-Directed DNA Methylation to Tandem Repeats

 

Abstract Tandem repeat sequences are frequently associated with gene silencing phenomena. The Arabidopsis thaliana FWA gene contains two tandem repeats and is an efficient target for RNA-directed de novo DNA methylation when it is transformed into plants. We showed that the FWA tandem repeats are necessary and sufficient for de novo DNA methylation and that … Continue readingResearch Summary: Two-Step Recruitment of RNA-Directed DNA Methylation to Tandem Repeats

Research Summary: Environmental perturbations lead to extensive directional shifts in RNA processing

 

ABSTRACT Environmental perturbations have large effects on both organismal and cellular traits, including gene expression, but the extent to which the environment affects RNA processing remains largely uncharacterized. Recent studies have identified a large number of genetic variants associated with variation in RNA processing that also have an important role in complex traits; yet we … Continue readingResearch Summary: Environmental perturbations lead to extensive directional shifts in RNA processing

Research Summary: Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex

 

ABSTRACT The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA. Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6, but it was unclear how … Continue readingResearch Summary: Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex

Research Summary: Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum

 

ABSTRACT RNA editing is a rare post-transcriptional event that provides cells with an additional level of gene expression regulation. It has been implicated in various processes including adaptation, viral defence and RNA interference; however, its potential role as a mechanism in acclimatization has just recently been recognised. Here, we show that RNA editing occurs in … Continue readingResearch Summary: Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum

Research Summary: Cellular mRNA Activates Transcription Elongation by Displacing 7SK RNA

 

ABSTRACT The positive transcription elongation factor P-TEFb is a pivotal regulator of gene expression in higher cells. Originally identified in Drosophila, attention was drawn to human P-TEFb by the discovery of its role as an essential cofactor for HIV-1 transcription. It is recruited to HIV transcription complexes by the viral transactivator Tat, and to cellular … Continue readingResearch Summary: Cellular mRNA Activates Transcription Elongation by Displacing 7SK RNA

Research Summary: Reduced APOBEC3H Variant Anti-Viral Activities Are Associated with Altered RNA Binding Activities

 

ABSTRACT APOBEC3H (A3H) is a member of the APOBEC3 family of proteins with varying activities against retroviruses and retrotransposons. The A3H gene contains several single nucleotide polymorphisms and up to seven haplotypes have been detected in humans. Although variations in anti-viral function among A3H haplotypes are not fully understood, only 15N105R-containing A3H variants are known … Continue readingResearch Summary: Reduced APOBEC3H Variant Anti-Viral Activities Are Associated with Altered RNA Binding Activities

Research Summary: Alternative Splicing and Extensive RNA Editing of Human TPH2 Transcripts

 

ABSTRACT Brain serotonin (5-HT) neurotransmission plays a key role in the regulation of mood and has been implicated in a variety of neuropsychiatric conditions. Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of 5-HT. Recently, we discovered a second TPH isoform (TPH2) in vertebrates, including man, which is predominantly expressed in brain, while … Continue readingResearch Summary: Alternative Splicing and Extensive RNA Editing of Human TPH2 Transcripts

Research Summary: Alternative Splicing and Extensive RNA Editing of Human TPH2 Transcripts

 

ABSTRACT Brain serotonin (5-HT) neurotransmission plays a key role in the regulation of mood and has been implicated in a variety of neuropsychiatric conditions. Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of 5-HT. Recently, we discovered a second TPH isoform (TPH2) in vertebrates, including man, which is predominantly expressed in brain, while … Continue readingResearch Summary: Alternative Splicing and Extensive RNA Editing of Human TPH2 Transcripts

Research Summary: A New Yeast Poly(A) Polymerase Complex Involved in RNA Quality Control

 

Abstract Eukaryotic cells contain several unconventional poly(A) polymerases in addition to the canonical enzymes responsible for the synthesis of poly(A) tails of nuclear messenger RNA precursors. The yeast protein Trf4p has been implicated in a quality control pathway that leads to the polyadenylation and subsequent exosome-mediated degradation of hypomethylated initiator tRNAMet (tRNAiMet). Here we show … Continue readingResearch Summary: A New Yeast Poly(A) Polymerase Complex Involved in RNA Quality Control

Research Summary: Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

 

Abstract Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from … Continue readingResearch Summary: Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

Research Summary: Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data

 

Abstract Recently, a novel approach has been developed to study gene expression in single cells with high time resolution using RNA Fluorescent In Situ Hybridization (FISH). The technique allows individual mRNAs to be counted with high accuracy in wild-type cells, but requires cells to be fixed; thus, each cell provides only a “snapshot” of gene … Continue readingResearch Summary: Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data

Research Summary: NTPase and 5′-RNA Triphosphatase Activities of Chikungunya Virus nsP2 Protein

 

ABSTRACT Chikungunya virus (CHIKV) is an insect borne virus (genus: Alphavirus) which causes acute febrile illness in humans followed by a prolonged arthralgic disease that affects the joints of the extremities. Re-emergence of the virus in the form of outbreaks in last 6–7 years has posed a serious public health problem. CHIKV has a positive … Continue readingResearch Summary: NTPase and 5′-RNA Triphosphatase Activities of Chikungunya Virus nsP2 Protein

Research Summary: Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions

 

Abstract The four-subunit Negative Elongation Factor (NELF) is a major regulator of RNA Polymerase II (Pol II) pausing. The subunit NELF-E contains a conserved RNA Recognition Motif (RRM) and is proposed to facilitate Poll II pausing through its association with nascent transcribed RNA. However, conflicting ideas have emerged for the function of its RNA binding … Continue readingResearch Summary: Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions

Research Summary: MOV10 RNA Helicase Is a Potent Inhibitor of Retrotransposition in Cells

 

Abstract MOV10 protein, a putative RNA helicase and component of the RNA–induced silencing complex (RISC), inhibits retrovirus replication. We show that MOV10 also severely restricts human LINE1 (L1), Alu, and SVA retrotransposons. MOV10 associates with the L1 ribonucleoprotein particle, along with other RNA helicases including DDX5, DHX9, DDX17, DDX21, and DDX39A. However, unlike MOV10, these … Continue readingResearch Summary: MOV10 RNA Helicase Is a Potent Inhibitor of Retrotransposition in Cells

Research Abstract: Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

 

Abstract Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs. We identified that RNA targets of Puf3 orthologs have been conserved over 100–500 million years of evolution in five eukaryotic lineages. Focusing on … Continue readingResearch Abstract: Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

Research Summary: RNA Interference to Suppress Flaviviral Encephalitis

 

Partial Text Mosquito-borne flaviviruses such as Japanese encephalitis virus (JEV) and West Nile virus (WNV) are two of the most important examples of emerging and resurging pathogens. Currently, there are no effective drugs available to treat these infections. Moreover, infections by diverse neurotropic flaviviruses are clinically indistinguishable, which makes it important to develop broad-based therapies … Continue readingResearch Summary: RNA Interference to Suppress Flaviviral Encephalitis

Research Summary: Discovering the Phylodynamics of RNA Viruses

 

Abstract ____________________________ Publisher: Public Library of Science Date Published: 26-October-2009 Author(s): Holmes E., Grenfell B. Link: https://doi.org/10.1371/journal.pcbi.1000505

Research Summary: Seeking Membranes: Positive-Strand RNA Virus Replication Complexes

 

Abstract How much do we really understand about how +RNA viruses usurp and transform the intracellular architecture of host cells when they replicate? ____________________________ Publisher: Public Library of Science Author(s): Denison M. Link: https://doi.org/10.1371/journal.pbio.0060270

Research Summary: Vasa-Like DEAD-Box RNA Helicases of Schistosoma mansoni

 

ABSTRACT Genome sequences are available for the human blood flukes, Schistosoma japonicum, S. mansoni and S. haematobium. Functional genomic approaches could aid in identifying the role and importance of these newly described schistosome genes. Transgenesis is established for functional genomics in model species, which can lead to gain- or loss-of-functions, facilitate vector-based RNA interference, and … Continue readingResearch Summary: Vasa-Like DEAD-Box RNA Helicases of Schistosoma mansoni

Research Summary: Biochemical Characterization of Enzyme Fidelity of Influenza A Virus RNA Polymerase Complex

 

ABSTRACT Background It is widely accepted that the highly error prone replication process of influenza A virus (IAV), together with viral genome assortment, facilitates the efficient evolutionary capacity of IAV. Therefore, it has been logically assumed that the enzyme responsible for viral RNA replication process, influenza virus type A RNA polymerase (IAV Pol), is a … Continue readingResearch Summary: Biochemical Characterization of Enzyme Fidelity of Influenza A Virus RNA Polymerase Complex

Research Summary: SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data

 

Abstract RNA-protein binding is critical to gene regulation, controlling fundamental processes including splicing, translation, localization and stability, and aberrant RNA-protein interactions are known to play a role in a wide variety of diseases. However, molecular understanding of RNA-protein interactions remains limited; in particular, identification of RNA motifs that bind proteins has long been challenging, especially … Continue readingResearch Summary: SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data

Research Summary: siRNA-Like Double-Stranded RNAs Are Specifically Protected Against Degradation in Human Cell Extract

 

ABSTRACT RNA interference (RNAi) is a set of intracellular pathways in eukaryotes that controls both exogenous and endogenous gene expression. The power of RNAi to knock down (silence) any gene of interest by the introduction of synthetic small-interfering (si)RNAs has afforded powerful insight into biological function through reverse genetic approaches and has borne a new … Continue readingResearch Summary: siRNA-Like Double-Stranded RNAs Are Specifically Protected Against Degradation in Human Cell Extract

Research Summary: Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

 

Abstract Clostridium difficile is an emergent pathogen, and the most common cause of nosocomial diarrhea. In an effort to understand the role of small noncoding RNAs (sRNAs) in C. difficile physiology and pathogenesis, we used an in silico approach to identify 511 sRNA candidates in both intergenic and coding regions. In parallel, RNA–seq and differential … Continue readingResearch Summary: Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

Research Summary: Telomeric Trans-Silencing: An Epigenetic Repression Combining RNA Silencing and Heterochromatin Formation

 

Abstract The study of P-element repression in Drosophila melanogaster led to the discovery of the telomeric Trans-Silencing Effect (TSE), a repression mechanism by which a transposon or a transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequence or TAS) has the capacity to repress in trans in the female germline, a homologous transposon, or transgene located … Continue readingResearch Summary: Telomeric Trans-Silencing: An Epigenetic Repression Combining RNA Silencing and Heterochromatin Formation

Research Summary: Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis

 

Abstract High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-Seq data. We introduce a Network-based method for … Continue readingResearch Summary: Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis

Research Summary: A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations

 

Abstract The development of modern and affordable sequencing technologies has allowed the study of viral populations to an unprecedented depth. This is of particular interest for the study of within-host RNA viral populations, where variation due to error-prone polymerases can lead to immune escape, antiviral resistance and adaptation to new host species. Methods to sequence … Continue readingResearch Summary: A Bayesian Approach to Analyse Genetic Variation within RNA Viral
Populations

Research Summary: Crumple: A Method for Complete Enumeration of All Possible Pseudoknot-Free RNA Secondary Structures

 

ABSTRACT The diverse landscape of RNA conformational space includes many canyons and crevices that are distant from the lowest minimum free energy valley and remain unexplored by traditional RNA structure prediction methods. A complete description of the entire RNA folding landscape can facilitate identification of biologically important conformations. The Crumple algorithm rapidly enumerates all possible … Continue readingResearch Summary: Crumple: A Method for Complete Enumeration of All Possible Pseudoknot-Free RNA Secondary Structures

Research Summary: Repertoire of Bovine miRNA and miRNA-Like Small Regulatory RNAs Expressed upon Viral Infection

 

ABSTRACT MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small RNAs characterized in mammals and to examine relationship between host miRNA expression and viral … Continue readingResearch Summary: Repertoire of Bovine miRNA and miRNA-Like Small Regulatory RNAs Expressed upon Viral Infection

Research Summary: Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21

 

ABSTRACT Hybridization- and tag-based technologies have been successfully used in Down syndrome to identify genes involved in various aspects of the pathogenesis. However, these technologies suffer from several limits and drawbacks and, to date, information about rare, even though relevant, RNA species such as long and small non-coding RNAs, is completely missing. Indeed, none of … Continue readingResearch Summary: Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in
Human Trisomy 21

Research Summary: Efficacy of a Novel Class of RNA Interference Therapeutic Agents

 

ABSTRACT RNA interference (RNAi) is being widely used in functional gene research and is an important tool for drug discovery. However, canonical double-stranded short interfering RNAs are unstable and induce undesirable adverse effects, and thus there is no currently RNAi-based therapy in the clinic. We have developed a novel class of RNAi agents, and evaluated … Continue readingResearch Summary: Efficacy of a Novel Class of RNA Interference Therapeutic Agents

Research Summary: Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

 

Abstract RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with … Continue readingResearch Summary: Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

Research Summary: Characterizing mRNA Interactions with RNA Granules during Translation Initiation Inhibition

 

ABSTRACT When cells experience environmental stresses, global translational arrest is often accompanied by the formation of stress granules (SG) and an increase in the number of p-bodies (PBs), which are thought to play a crucial role in the regulation of eukaryotic gene expression through the control of mRNA translation and degradation. SGs and PBs have … Continue readingResearch Summary: Characterizing mRNA Interactions with RNA Granules during Translation
Initiation Inhibition

Research Abstract: RNA stores tau reversibly in complex coacervates

 

Abstract Nonmembrane-bound organelles that behave like liquid droplets are widespread among eukaryotic cells. Their dysregulation appears to be a critical step in several neurodegenerative conditions. Here, we report that tau protein, the primary constituent of Alzheimer neurofibrillary tangles, can form liquid droplets and therefore has the necessary biophysical properties to undergo liquid-liquid phase separation (LLPS) … Continue readingResearch Abstract: RNA stores tau reversibly in complex coacervates

Research Summary: Gene Expression Profiling of Liver Cancer Stem Cells by RNA-Sequencing

 

ABSTRACT Background Accumulating evidence supports that tumor growth and cancer relapse are driven by cancer stem cells. Our previous work has demonstrated the existence of CD90+ liver cancer stem cells (CSCs) in hepatocellular carcinoma (HCC). Nevertheless, the characteristics of these cells are still poorly understood. In this study, we employed a more sensitive RNA-sequencing (RNA-Seq) … Continue readingResearch Summary: Gene Expression Profiling of Liver Cancer Stem Cells by RNA-Sequencing

Research Summary: RNA Is an Integral Component of Chromatin that Contributes to Its Structural Organization

 

ABSTRACT Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants … Continue readingResearch Summary: RNA Is an Integral Component of Chromatin that Contributes to Its Structural Organization

Research Summary: Tissue-Specific Differences in Human Transfer RNA Expression

 

Abstract Over 450 transfer RNA (tRNA) genes have been annotated in the human genome. Reliable quantitation of tRNA levels in human samples using microarray methods presents a technical challenge. We have developed a microarray method to quantify tRNAs based on a fluorescent dye-labeling technique. The first-generation tRNA microarray consists of 42 probes for nuclear encoded … Continue readingResearch Summary: Tissue-Specific Differences in Human Transfer RNA Expression

Research Summary: The H19 Non-Coding RNA Is Essential for Human Tumor Growth

 

ABSTRACT Background Mutations and epigenetic aberrant signaling of growth factors pathways contribute to carcinogenesis. Recent studies reveal that non-coding RNAs are controllers of gene expression. H19 is an imprinted gene that demonstrates maternal monoallelic expression without a protein product; although its expression is shut off in most tissues postnatally, it is re-activated during adult tissue … Continue readingResearch Summary: The H19 Non-Coding RNA Is Essential for Human Tumor Growth

Research Summary: Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks

 

Abstract Bacteria possess networks of small RNAs (sRNAs) that are important for modulating gene expression. At the center of many of these sRNA networks is the Hfq protein. Hfq’s role is to quickly match cognate sRNAs and target mRNAs from among a large number of possible combinations and anneal them to form duplexes. Here we … Continue readingResearch Summary: Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks

Research Summary: Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

 

Abstract The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional commonalities define classes of RNAs that are characterized by structural similarities, and typically consist of multiple RNA families. Recent advances in high-throughput transcriptomics and comparative … Continue readingResearch Summary: Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

Research Summary: Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana

 

Abstract Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution. This is due in part to scant data on epigenetic variation among natural populations. In plants, small interfering RNA (siRNA) is involved in both the initiation and … Continue readingResearch Summary: Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana

Research Summary: Predicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteins

 

ABSTRACT Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary … Continue readingResearch Summary: Predicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteins

Research Summary: Epigenetic Engineering of Ribosomal RNA Genes Enhances Protein Production

 

ABSTRACT Selection of mammalian high-producer cell lines remains a major challenge for the biopharmaceutical manufacturing industry. Ribosomal RNA (rRNA) genes encode the major component of the ribosome but many rRNA gene copies are not transcribed [1]–[5] due to epigenetic silencing by the nucleolar remodelling complex (NoRC) [6], which may limit the cell’s full production capacity. … Continue readingResearch Summary: Epigenetic Engineering of Ribosomal RNA Genes Enhances Protein Production

Research Summary: Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates

 

ABSTRACT The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in … Continue readingResearch Summary: Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates

Research Abstract: Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

 

Abstract Genome-wide rhythms in RNA polymerase II loading and dynamic chromatin remodeling underlie periodic gene expression during diurnal cycles in the mouse liver. ____________________________ Publisher: Public Library of Science Date Published: 27-November-2012 Author(s): Le Martelot G., Canella D., Symul L., Migliavacca E., Gilardi F., Liechti R., Martin O., Harshman K., Delorenzi M., Desvergne B., Herr … Continue readingResearch Abstract: Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

Research Summary: A Novel RNA Transcript with Antiapoptotic Function Is Silenced in Fragile X Syndrome

 

ABSTRACT Several genome-wide transcriptomics efforts have shown that a large percentage of the mammalian genome is transcribed into RNAs, however, only a small percentage (1–2%) of these RNAs is translated into proteins. Currently there is an intense interest in characterizing the function of the different classes of noncoding RNAs and their relevance to human disease. … Continue readingResearch Summary: A Novel RNA Transcript with Antiapoptotic Function Is Silenced in Fragile X Syndrome

Research Summary: Inhibition of Pre-mRNA Splicing by a Synthetic Blom7α-Interacting Small RNA

 

ABSTRACT Originally the novel protein Blom7α was identified as novel pre-mRNA splicing factor that interacts with SNEVPrp19/Pso4, an essential protein involved in extension of human endothelial cell life span, DNA damage repair, the ubiquitin-proteasome system, and pre-mRNA splicing. Blom7α belongs to the heteronuclear ribonucleoprotein K homology (KH) protein family, displaying 2 KH domains, a well … Continue readingResearch Summary: Inhibition of Pre-mRNA Splicing by a Synthetic Blom7α-Interacting Small RNA

Research Summary: Active RNA Polymerases: Mobile or Immobile Molecular Machines?

 

Abstract Although it is widely assumed that active RNA polymerase tracks along its template, we find that DNA, not the polymerase, moves, suggesting that polymerase works by reeling in the template. ____________________________ Publisher: Public Library of Science Author(s): Papantonis A., Larkin J., Wada Y., Ohta Y., Ihara S., Kodama T., Cook P. Link: https://doi.org/10.1371/journal.pbio.1000419

Research Summary: DNA Binding of Centromere Protein C (CENPC) Is Stabilized by Single-Stranded RNA

 

Abstract Centromeres are the attachment points between the genome and the cytoskeleton: centromeres bind to kinetochores, which in turn bind to spindles and move chromosomes. Paradoxically, the DNA sequence of centromeres has little or no role in perpetuating kinetochores. As such they are striking examples of genetic information being transmitted in a manner that is … Continue readingResearch Summary: DNA Binding of Centromere Protein C (CENPC) Is Stabilized by Single-Stranded RNA

Research Summary: Cloning of the Quail PIWI Gene and Characterization of PIWI Binding to Small RNAs

 

ABSTRACT The PIWI protein regulates gene expression at the epigenetic and post-transcriptional level with a variety of endogenous small non-coding RNAs. In poultry, the biological function of the PIWI protein and PIWI binding to small RNAs had not been determined. The present study cloned and analyzed the sequences of the PIWIL1 protein. We also characterized … Continue readingResearch Summary: Cloning of the Quail PIWI Gene and Characterization of PIWI Binding to Small RNAs

Research Summary: Evolution of Susceptibility to Ingested Double-Stranded RNAs in Caenorhabditis Nematodes

 

ABSTRACT Background The nematode Caenorhabditis elegans is able to take up external double-stranded RNAs (dsRNAs) and mount an RNA interference response, leading to the inactivation of specific gene expression. The uptake of ingested dsRNAs into intestinal cells has been shown to require the SID-2 transmembrane protein in C. elegans. By contrast, C. briggsae was shown … Continue readingResearch Summary: Evolution of Susceptibility to Ingested Double-Stranded RNAs in Caenorhabditis Nematodes

Research Summary: Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

 

ABSTRACT Background Computational analysis of cDNA sequences from multiple organisms suggests that a large portion of transcribed DNA does not code for a functional protein. In mammals, noncoding transcription is abundant, and often results in functional RNA molecules that do not appear to encode proteins. Many long noncoding RNAs (lncRNAs) appear to have epigenetic regulatory … Continue readingResearch Summary: Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

Research Summary: A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

 

Abstract Noncoding RNAs (ncRNAs) are important functional RNAs that do not code for proteins. We present a highly efficient computational pipeline for discovering cis-regulatory ncRNA motifs de novo. The pipeline differs from previous methods in that it is structure-oriented, does not require a multiple-sequence alignment as input, and is capable of detecting RNA motifs with … Continue readingResearch Summary: A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

Research Summary: SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

 

Abstract Computational methods for predicting evolutionarily conserved rather than thermodynamic RNA structures have recently attracted increased interest. These methods are indispensable not only for elucidating the regulatory roles of known RNA transcripts, but also for predicting RNA genes. It has been notoriously difficult to devise them to make the best use of the available data … Continue readingResearch Summary: SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

Research Summary: Crystal Structure of the Dengue Virus Methyltransferase Bound to a 5′-Capped Octameric RNA

 

ABSTRACT The N-terminal domain of the flavivirus NS5 protein functions as a methyltransferase (MTase). It sequentially methylates the N7 and 2′-O positions of the viral RNA cap structure (GpppA→7meGpppA→7meGpppA2′-O-me). The same NS5 domain could also have a guanylyltransferase activity (GTP+ppA-RNA→GpppA). The mechanism by which this protein domain catalyzes these three distinct functions is currently unknown. … Continue readingResearch Summary: Crystal Structure of the Dengue Virus Methyltransferase Bound to a 5′-Capped Octameric RNA

Research Summary: Correction: RNA-Binding Protein FXR1 Regulates p21 and TERC RNA to Bypass p53-Mediated Cellular Senescence in OSCC

 

Partial Text In panel G of ….. ____________________________ Publisher: Public Library of Science Date Published: 26-October-2016 Author(s): Majumder M., House R., Palanisamy N., Qie S., Day T., Neskey D., Diehl J., Palanisamy V. Link: https://doi.org/10.1371/journal.pgen.1006411

Research Summary: Widespread A-to-I RNA Editing of Alu-Containing mRNAs in the Human Transcriptome

 

Abstract RNA editing by adenosine deamination generates RNA and protein diversity through the posttranscriptional modification of single nucleotides in RNA sequences. Few mammalian A-to-I edited genes have been identified despite evidence that many more should exist. Here we identify intramolecular pairs of Alu elements as a major target for editing in the human transcriptome. An … Continue readingResearch Summary: Widespread A-to-I RNA Editing of Alu-Containing mRNAs in the Human Transcriptome

Research Summary: Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing

 

Abstract In flowering plants, mitochondrial and chloroplast mRNAs are edited by C-to-U base modification. In plant organelles, RNA editing appears to be generally a correcting mechanism that restores the proper function of the encoded product. Members of the Arabidopsis RNA editing-Interacting Protein (RIP) family have been recently shown to be essential components of the plant … Continue readingResearch Summary: Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing

Research Summary: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”

 

ABSTRACT Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole … Continue readingResearch Summary: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”

Research Summary: Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle

 

Abstract Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and … Continue readingResearch Summary: Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle

Research Summary: Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa Carbon Catabolite Repression

 

ABSTRACT Carbon Catabolite repression (CCR) allows a fast adaptation of Bacteria to changing nutrient supplies. The Pseudomonas aeruginosa (PAO1) catabolite repression control protein (Crc) was deemed to act as a translational regulator, repressing functions involved in uptake and utilization of carbon sources. However, Crc of PAO1 was recently shown to be devoid of RNA binding … Continue readingResearch Summary: Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa Carbon Catabolite Repression

Research Summary: Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

 

Abstract HIV and related primate lentiviruses possess single-stranded RNA genomes. Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures. The structures of these elements are still not fully understood, and additional functional elements likely exist … Continue readingResearch Summary: Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

Research Summary: High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs

 

ABSTRACT Background Diverse bacterial genomes encode numerous small non-coding RNAs (sRNAs) that regulate myriad biological processes. While bioinformatic algorithms have proven effective in identifying sRNA-encoding loci, the lack of tools and infrastructure with which to execute these computationally demanding algorithms has limited their utilization. Genome-wide predictions of sRNA-encoding genes have been conducted in less than … Continue readingResearch Summary: High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs

Research Summary: A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi

 

ABSTRACT The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common … Continue readingResearch Summary: A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi

Research Summary: The Mechanism for RNA Recognition by ANTAR Regulators of Gene Expression

 

Abstract ANTAR proteins are widespread bacterial regulatory proteins that have RNA–binding output domains and utilize antitermination to control gene expression at the post-initiation level. An ANTAR protein, EutV, regulates the ethanolamine-utilization genes (eut) in Enterococcus faecalis. Using this system, we present genetic and biochemical evidence of a general mechanism of antitermination used by ANTARs, including … Continue readingResearch Summary: The Mechanism for RNA Recognition by ANTAR Regulators of Gene Expression

Research Summary: Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA

 

ABSTRACT Background The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. … Continue readingResearch Summary: Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA

Research Summary: The Complex Exogenous RNA Spectra in Human Plasma: An Interface with Human Gut Biota?

 

ABSTRACT Human plasma has long been a rich source for biomarker discovery. It has recently become clear that plasma RNA molecules, such as microRNA, in addition to proteins are common and can serve as biomarkers. Surveying human plasma for microRNA biomarkers using next generation sequencing technology, we observed that a significant fraction of the circulating … Continue readingResearch Summary: The Complex Exogenous RNA Spectra in Human Plasma: An Interface with Human Gut Biota?

Research Summary: Two Oppositely Localised Frizzled RNAs as Axis Determinants in a Cnidarian Embryo

 

Abstract In phylogenetically diverse animals, including the basally diverging cnidarians, “determinants” localised within the egg are responsible for directing development of the embryonic body plan. Many such determinants are known to regulate the Wnt signalling pathway, leading to regionalised stabilisation of the transcriptional coregulator β-catenin; however, the only strong molecular candidate for a Wnt-activating determinant … Continue readingResearch Summary: Two Oppositely Localised Frizzled RNAs as Axis Determinants in a Cnidarian Embryo

Research Summary: Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

 

ABSTRACT RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family … Continue readingResearch Summary: Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

Research Summary: Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

 

Abstract While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent … Continue readingResearch Summary: Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

Research Summary: The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing

 

ABSTRACT In this study, we evaluated how gene expression differs in mature Pseudomonas aeruginosa biofilms as opposed to planktonic cells by the use of RNA sequencing technology that gives rise to both quantitative and qualitative information on the transcriptome. Although a large proportion of genes were consistently regulated in both the stationary phase and biofilm … Continue readingResearch Summary: The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing

Research Summary: The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis

 

ABSTRACT TRAM is a conserved domain among RNA modification proteins that are widely distributed in various organisms. In Archaea, TRAM occurs frequently as a standalone protein with in vitro RNA chaperone activity; however, its biological significance and functional mechanism remain unknown. This work demonstrated that TRAM0076 is an abundant standalone TRAM protein in the genetically … Continue readingResearch Summary: The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis

Research Summary: Characterization of the Zika virus induced small RNA response in Aedes aegypti cells

 

ABSTRACT RNA interference (RNAi) controls arbovirus infections in mosquitoes. Two different RNAi pathways are involved in antiviral responses: the PIWI-interacting RNA (piRNA) and exogenous short interfering RNA (exo-siRNA) pathways, which are characterized by the production of virus-derived small RNAs of 25–29 and 21 nucleotides, respectively. The exo-siRNA pathway is considered to be the key mosquito … Continue readingResearch Summary: Characterization of the Zika virus induced small RNA response in Aedes aegypti cells

Research Summary: Mediator Directs Co-transcriptional Heterochromatin Assembly by RNA Interference-Dependent and -Independent Pathways

 

Abstract Heterochromatin at the pericentromeric repeats in fission yeast is assembled and spread by an RNAi-dependent mechanism, which is coupled with the transcription of non-coding RNA from the repeats by RNA polymerase II. In addition, Rrp6, a component of the nuclear exosome, also contributes to heterochromatin assembly and is coupled with non-coding RNA transcription. The … Continue readingResearch Summary: Mediator Directs Co-transcriptional Heterochromatin Assembly by RNA Interference-Dependent and -Independent Pathways

Research Summary: Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing

 

ABSTRACT Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint … Continue readingResearch Summary: Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing

Research Summary: PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks

 

Abstract RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, … Continue readingResearch Summary: PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks

Research Summary: Intradermal Electroporation of Naked Replicon RNA Elicits Strong Immune Responses

 

ABSTRACT RNA-based vaccines represent an interesting immunization modality, but suffer from poor stability and a lack of efficient and clinically feasible delivery technologies. This study evaluates the immunogenic potential of naked in vitro transcribed Semliki Forest virus replicon RNA (RREP) delivered intradermally in combination with electroporation. Replicon-immunized mice showed a strong cellular and humoral response, … Continue readingResearch Summary: Intradermal Electroporation of Naked Replicon RNA Elicits Strong Immune Responses

Research Summary: Determinants of RNA Quality from FFPE Samples

 

ABSTRACT The large archives of formalin-fixed paraffin-embedded (FFPE) tissue specimens that exist are a highly valuable source of sample material for molecular biological analysis, including gene expression profiling. However, current data on adverse effects of standard pathological practice on the usefulness of biomolecular analytes obtained from such archived specimens is largely anecdotal. Here, we present … Continue readingResearch Summary: Determinants of RNA Quality from FFPE Samples

Research Summary: Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish

 

ABSTRACT Fragile X syndrome (FXS) is the most frequent inherited form of mental retardation. The cause for this X-linked disorder is the silencing of the fragile X mental retardation 1 (fmr1) gene and the absence of the fragile X mental retardation protein (Fmrp). The RNA-binding protein Fmrp represses protein translation, particularly in synapses. In Drosophila, … Continue readingResearch Summary: Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish

Research Summary: The RNA Binding Protein Csx1 Promotes Sexual Differentiation in Schizosaccharomyces pombe

 

ABSTRACT Sexual differentiation is a highly regulated process in the fission yeast Schizosaccharomyces pombe and is triggered by nutrient depletion, mainly nitrogen source. One of the key regulatory proteins in fission yeast sexual differentiation is the transcription factor Ste11. Ste11 regulates the transcription of many genes required for the initial steps of conjugation and meiosis, … Continue readingResearch Summary: The RNA Binding Protein Csx1 Promotes Sexual Differentiation in Schizosaccharomyces pombe

Research Summary: Computational Detection and Functional Analysis of Human Tissue-Specific A-to-I RNA Editing

 

ABSTRACT A-to-I RNA editing is a widespread post-transcriptional modification event in vertebrates. It could increase transcriptome and proteome diversity through recoding the genomic information and cross-linking other regulatory events, such as those mediated by alternative splicing, RNAi and microRNA (miRNA). Previous studies indicated that RNA editing can occur in a tissue-specific manner in response to … Continue readingResearch Summary: Computational Detection and Functional Analysis of Human Tissue-Specific A-to-I RNA Editing

Research Summary: Regulatory BC1 RNA and the Fragile X Mental Retardation Protein: Convergent Functionality in Brain

 

ABSTRACT Background BC RNAs and the fragile X mental retardation protein (FMRP) are translational repressors that have been implicated in the control of local protein synthesis at the synapse. Work with BC1 and Fmr1 animal models has revealed that phenotypical consequences resulting from the absence of either BC1 RNA or FMRP are remarkably similar. To … Continue readingResearch Summary: Regulatory BC1 RNA and the Fragile X Mental Retardation Protein: Convergent Functionality in Brain

Research Summary: Why are RNA virus mutation rates so damn high?

 

Abstract The high mutation rate of RNA viruses is credited with their evolvability and virulence. This Primer, however, discusses recent evidence that this is, in part, a byproduct of selection for faster genomic replication. ____________________________ Publisher: Public Library of Science Date Published: 13-August-2018 Author(s): Duffy S. Link: https://doi.org/10.1371/journal.pbio.3000003

Research Summary: Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines

 

Abstract RIKEN’s FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever more transcripts that do not code for proteins have been identified by transcriptome studies, in general. Increasing evidence points to the important cellular roles of such … Continue readingResearch Summary: Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines

Research Summary: BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

 

Abstract High-throughput RNA-seq technology has provided an unprecedented opportunity to reveal the very complex structures of transcriptomes. However, it is an important and highly challenging task to assemble vast amounts of short RNA-seq reads into transcriptomes with alternative splicing isoforms. In this study, we present a novel de novo assembler, BinPacker, by modeling the transcriptome … Continue readingResearch Summary: BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

Research Summary: A Pol V–Mediated Silencing, Independent of RNA–Directed DNA Methylation, Applies to 5S rDNA

 

Abstract The plant-specific RNA polymerases Pol IV and Pol V are essential to RNA–directed DNA methylation (RdDM), which also requires activities from RDR2 (RNA–Dependent RNA Polymerase 2), DCL3 (Dicer-Like 3), AGO4 (Argonaute), and DRM2 (Domains Rearranged Methyltransferase 2). RdDM is dedicated to the methylation of target sequences which include transposable elements, regulatory regions of several … Continue readingResearch Summary: A Pol V–Mediated Silencing, Independent of RNA–Directed DNA Methylation, Applies to 5S rDNA

Research Abstract: Long Noncoding RNAs Promote Transcriptional Poising of Inducible Genes

 

Abstract The GAL cluster-associated long non-coding RNAs (lncRNAs) promote rapid induction of GAL genes in budding yeast, thereby promoting a faster switch in transcriptional programs when needed. ____________________________ Publisher: Public Library of Science Date Published: 19-November-2013 Author(s): Cloutier S., Wang S., Ma W., Petell C., Tran E. Link: https://doi.org/10.1371/journal.pbio.1001715

Research Summary: Differential and convergent utilization of autophagy components by positive-strand RNA viruses

 

Abstract Many viruses interface with the autophagy pathway, a highly conserved process for recycling cellular components. For three viral infections in which autophagy constituents are proviral (poliovirus, dengue, and Zika), we developed a panel of knockouts (KOs) of autophagy-related genes to test which components of the canonical pathway are utilized. We discovered that each virus … Continue readingResearch Summary: Differential and convergent utilization of autophagy components by positive-strand RNA viruses

Research Summary: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp

 

ABSTRACT Gill-associated virus (GAV) infects Penaeus monodon shrimp and is the type species okavirus in the Roniviridae, the only invertebrate nidoviruses known currently. Electrophoretic mobility shift assays (EMSAs) using His6-tagged full-length and truncated proteins were employed to examine the nucleic acid binding properties of the GAV nucleocapsid (N) protein in vitro. The EMSAs showed full-length … Continue readingResearch Summary: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp

Research Summary: The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate

 

Abstract Homeostasis of most adult tissues is maintained by balancing stem cell self-renewal and differentiation, but whether post-transcriptional mechanisms can regulate this process is unknown. Here, we identify that an RNA methyltransferase (Misu/Nsun2) is required to balance stem cell self-renewal and differentiation in skin. In the epidermis, this methyltransferase is found in a defined sub-population … Continue readingResearch Summary: The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate

Research Summary: Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae

 

Abstract Non-coding RNA (ncRNA) play an important and varied role in cellular function. A significant amount of research has been devoted to computational prediction of these genes from genomic sequence, but the ability to do so has remained elusive due to a lack of apparent genomic features. In this work, thermodynamic stability of ncRNA structural … Continue readingResearch Summary: Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae

Research Summary: The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs

 

Abstract Small RNAs regulate diverse biological processes by directing effector proteins called Argonautes to silence complementary mRNAs. Maturation of some classes of small RNAs involves terminal 2′-O-methylation to prevent degradation. This modification is catalyzed by members of the conserved HEN1 RNA methyltransferase family. In animals, Piwi-interacting RNAs (piRNAs) and some endogenous and exogenous small interfering … Continue readingResearch Summary: The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs

Research Summary: Crystal Structure of the S. solfataricus Archaeal Exosome Reveals Conformational Flexibility in the RNA-Binding Ring

 

ABSTRACT Background The exosome complex is an essential RNA 3′-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. Methodology/Principal Findings Here we report an asymmetric 2.9 Å Sulfolobus solfataricus archaeal exosome structure in which the … Continue readingResearch Summary: Crystal Structure of the S. solfataricus Archaeal Exosome Reveals Conformational Flexibility in the RNA-Binding Ring

Research Summary: Crystal Structure of the S. solfataricus Archaeal Exosome Reveals Conformational Flexibility in the RNA-Binding Ring

 

ABSTRACT Background The exosome complex is an essential RNA 3′-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. Methodology/Principal Findings Here we report an asymmetric 2.9 Å Sulfolobus solfataricus archaeal exosome structure in which the … Continue readingResearch Summary: Crystal Structure of the S. solfataricus Archaeal Exosome Reveals Conformational Flexibility in the RNA-Binding Ring

Research Summary: Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome

 

ABSTRACT The mitochondrial genome of Trypanosoma brucei contains many cryptogenes that must be extensively edited following transcription. The RNA editing process is directed by guide RNAs (gRNAs) that encode the information for the specific insertion and deletion of uridylates required to generate translatable mRNAs. We have deep sequenced the gRNA transcriptome from the bloodstream form … Continue readingResearch Summary: Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome

Research Summary: De Novo Polymerase Activity and Oligomerization of Hepatitis C Virus RNA-Dependent RNA-Polymerases from Genotypes 1 to 5

 

ABSTRACT Hepatitis C virus (HCV) shows a great geographical diversity reflected in the high number of circulating genotypes and subtypes. The response to HCV treatment is genotype specific, with the predominant genotype 1 showing the lowest rate of sustained virological response. Virally encoded enzymes are candidate targets for intervention. In particular, promising antiviral molecules are … Continue readingResearch Summary: De Novo Polymerase Activity and Oligomerization of Hepatitis C Virus RNA-Dependent RNA-Polymerases from Genotypes 1 to 5

Research Summary: IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis

 

Abstract Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles … Continue readingResearch Summary: IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis

Research Summary: C6/36 Aedes albopictus Cells Have a Dysfunctional Antiviral RNA Interference Response

 

ABSTRACT Mosquitoes rely on RNA interference (RNAi) as their primary defense against viral infections. To this end, the combination of RNAi and invertebrate cell culture systems has become an invaluable tool in studying virus-vector interactions. Nevertheless, a recent study failed to detect an active RNAi response to West Nile virus (WNV) infection in C6/36 (Aedes … Continue readingResearch Summary: C6/36 Aedes albopictus Cells Have a Dysfunctional Antiviral RNA Interference Response

Research Abstract: Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages

 

Abstract Small RNA pathways act at the front line of defence against transposable elements across the Eukaryota. In animals, Piwi interacting small RNAs (piRNAs) are a crucial arm of this defence. However, the evolutionary relationships among piRNAs and other small RNA pathways targeting transposable elements are poorly resolved. To address this question we sequenced small … Continue readingResearch Abstract: Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages

Research Summary: Nutrient-Regulated Antisense and Intragenic RNAs Modulate a Signal Transduction Pathway in Yeast

 

Abstract The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability. The PHO system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes (PHO genes) is expressed to activate inorganic phosphate (Pi) metabolism for adaptation to Pi starvation. … Continue readingResearch Summary: Nutrient-Regulated Antisense and Intragenic RNAs Modulate a Signal Transduction Pathway in Yeast

Research Summary: Parasite specific 7SL-derived small RNA is an effective target for diagnosis of active trypanosomiasis infection

 

ABSTRACT Human and animal African trypanosomiasis (HAT & AAT, respectively) remain a significant health and economic issue across much of sub-Saharan Africa. Effective control of AAT and potential eradication of HAT requires affordable, sensitive and specific diagnostic tests that can be used in the field. Small RNAs in the blood or serum are attractive disease … Continue readingResearch Summary: Parasite specific 7SL-derived small RNA is an effective target for diagnosis of active trypanosomiasis infection

Research Summary: The Prefoldin Bud27 Mediates the Assembly of the Eukaryotic RNA Polymerases in an Rpb5-Dependent Manner

 

Abstract The unconventional prefoldin URI/RMP, in humans, and its orthologue in yeast, Bud27, have been proposed to participate in the biogenesis of the RNA polymerases. However, this role of Bud27 has not been confirmed and is poorly elucidated. Our data help clarify the mechanisms governing biogenesis of the three eukaryotic RNA pols. We show evidence … Continue readingResearch Summary: The Prefoldin Bud27 Mediates the Assembly of the Eukaryotic RNA Polymerases in an Rpb5-Dependent Manner

Research Summary: Control of Signaling in a MAP-kinase Pathway by an RNA-Binding Protein

 

ABSTRACT Signaling-protein mRNAs tend to have long untranslated regions (UTRs) containing binding sites for RNA-binding proteins regulating gene expression. Here we show that a PUF-family RNA-binding protein, Mpt5, represses the yeast MAP-kinase pathway controlling differentiation to the filamentous form. Mpt5 represses the protein levels of two pathway components, the Ste7 MAP-kinase kinase and the Tec1 … Continue readingResearch Summary: Control of Signaling in a MAP-kinase Pathway by an RNA-Binding Protein

Research Summary: A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes

 

ABSTRACT Hundreds of RNA-binding proteins (RBPs) control diverse aspects of post-transcriptional gene regulation. To identify novel and unconventional RBPs, we probed high-density protein microarrays with fluorescently labeled RNA and selected 200 proteins that reproducibly interacted with different types of RNA from budding yeast Saccharomyces cerevisiae. Surprisingly, more than half of these proteins represent previously known … Continue readingResearch Summary: A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes

Research Summary: Impaired Embryonic Development in Mice Overexpressing the RNA-Binding Protein TIAR

 

ABSTRACT Background TIA-1-related (TIAR) protein is a shuttling RNA-binding protein involved in several steps of RNA metabolism. While in the nucleus TIAR participates to alternative splicing events, in the cytoplasm TIAR acts as a translational repressor on specific transcripts such as those containing AU-Rich Elements (AREs). Due to its ability to assemble abortive pre-initiation complexes … Continue readingResearch Summary: Impaired Embryonic Development in Mice Overexpressing the RNA-Binding Protein TIAR

Research Summary: Estimating the Impact of Plasma HIV-1 RNA Reductions on Heterosexual HIV-1 Transmission Risk

 

ABSTRACT Background The risk of sexual transmission of HIV-1 is strongly associated with the level of HIV-1 RNA in plasma making reduction in HIV-1 plasma levels an important target for HIV-1 prevention interventions. A quantitative understanding of the relationship of plasma HIV-1 RNA and HIV-1 transmission risk could help predict the impact of candidate HIV-1 … Continue readingResearch Summary: Estimating the Impact of Plasma HIV-1 RNA Reductions on Heterosexual HIV-1 Transmission Risk

Research Summary: RNA Pol II Promotes Transcription of Centromeric Satellite DNA in Beetles

 

ABSTRACT Transcripts of centromeric satellite DNAs are known to play a role in heterochromatin formation as well as in establishment of the kinetochore. However, little is known about basic mechanisms of satellite DNA expression within constitutive heterochromatin and its regulation. Here we present comprehensive analysis of transcription of abundant centromeric satellite DNA, PRAT from beetle … Continue readingResearch Summary: RNA Pol II Promotes Transcription of Centromeric Satellite DNA in Beetles

Research Summary: AMPK regulates germline stem cell quiescence and integrity through an endogenous small RNA pathway

 

Abstract During suboptimal growth conditions, Caenorhabditis elegans larvae undergo a global developmental arrest called “dauer.” During this stage, the germline stem cells (GSCs) become quiescent in an AMP-activated Protein Kinase (AMPK)-dependent manner, and in the absence of AMPK, the GSCs overproliferate and lose their reproductive capacity, leading to sterility when mutant animals resume normal growth. … Continue readingResearch Summary: AMPK regulates germline stem cell quiescence and integrity through an endogenous small RNA pathway

Research Summary: Efficient Cellular Release of Rift Valley Fever Virus Requires Genomic RNA

 

ABSTRACT The Rift Valley fever virus is responsible for periodic, explosive epizootics throughout sub-Saharan Africa. The development of therapeutics targeting this virus is difficult due to a limited understanding of the viral replicative cycle. Utilizing a virus-like particle system, we have established roles for each of the viral structural components in assembly, release, and virus … Continue readingResearch Summary: Efficient Cellular Release of Rift Valley Fever Virus Requires Genomic RNA

Research Summary: Protein Localization with Flexible DNA or RNA

 

ABSTRACT Localization of activity is ubiquitous in life, and also within sub-cellular compartments. Localization provides potential advantages as different proteins involved in the same cellular process may supplement each other on a fast timescale. It might also prevent proteins from being active in other regions of the cell. However localization is at odds with the … Continue readingResearch Summary: Protein Localization with Flexible DNA or RNA

Research Summary: The TAL Effector PthA4 Interacts with Nuclear Factors Involved in RNA-Dependent Processes Including a HMG Protein That Selectively Binds Poly(U) RNA

 

ABSTRACT Plant pathogenic bacteria utilize an array of effector proteins to cause disease. Among them, transcriptional activator-like (TAL) effectors are unusual in the sense that they modulate transcription in the host. Although target genes and DNA specificity of TAL effectors have been elucidated, how TAL proteins control host transcription is poorly understood. Previously, we showed … Continue readingResearch Summary: The TAL Effector PthA4 Interacts with Nuclear Factors Involved in RNA-Dependent Processes Including a HMG Protein That Selectively Binds Poly(U) RNA

Research Summary: Non-coding roX RNAs Prevent the Binding of the MSL-complex to Heterochromatic Regions

 

ABSTRACT Long non-coding RNAs contribute to dosage compensation in both mammals and Drosophila by inducing changes in the chromatin structure of the X-chromosome. In Drosophila melanogaster, roX1 and roX2 are long non-coding RNAs that together with proteins form the male-specific lethal (MSL) complex, which coats the entire male X-chromosome and mediates dosage compensation by increasing … Continue readingResearch Summary: Non-coding roX RNAs Prevent the Binding of the MSL-complex to Heterochromatic Regions

Research Summary: Processivity and Coupling in Messenger RNA Transcription

 

ABSTRACT Background The complexity of messenger RNA processing is now being uncovered by experimental techniques that are capable of detecting individual copies of mRNA in cells, and by quantitative real-time observations that reveal the kinetics. This processing is commonly modelled by permitting mRNA to be transcribed only when the promoter is in the on state. … Continue readingResearch Summary: Processivity and Coupling in Messenger RNA Transcription

Research Summary: Processivity and Coupling in Messenger RNA Transcription

 

ABSTRACT Background The complexity of messenger RNA processing is now being uncovered by experimental techniques that are capable of detecting individual copies of mRNA in cells, and by quantitative real-time observations that reveal the kinetics. This processing is commonly modelled by permitting mRNA to be transcribed only when the promoter is in the on state. … Continue readingResearch Summary: Processivity and Coupling in Messenger RNA Transcription

Research Summary: Selection for Robustness in Mutagenized RNA Viruses

 

Abstract Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Whether robustness can be directly favored by natural selection remains controversial. Theory and in silico experiments predict that, at high mutation rates, slow-replicating genotypes can potentially outcompete faster counterparts if they benefit from a higher robustness. Here, we … Continue readingResearch Summary: Selection for Robustness in Mutagenized RNA Viruses

Research Summary: Stochastic principles governing alternative splicing of RNA

 

Abstract The dominance of the major transcript isoform relative to other isoforms from the same gene generated by alternative splicing (AS) is essential to the maintenance of normal cellular physiology. However, the underlying principles that determine such dominance remain unknown. Here, we analyzed the physical AS process and found that it can be modeled by … Continue readingResearch Summary: Stochastic principles governing alternative splicing of RNA

Research Summary: An Enzyme That Oversees RNA Quality Control

 

Abstract ____________________________ Publisher: Public Library of Science Author(s): Link: https://doi.org/10.1371/journal.pbio.0030191

Research Summary: A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription

 

ABSTRACT Transcription of the several hundred of mouse and human Ribosomal RNA (rRNA) genes accounts for the majority of RNA synthesis in the cell nucleus and is the determinant of cytoplasmic ribosome abundance, a key factor in regulating gene expression. The rRNA genes, referred to globally as the rDNA, are clustered as direct repeats at … Continue readingResearch Summary: A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription

Research Summary: Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing

 

ABSTRACT Background The ciliated protozoan Tetrahymena thermophila is a well-studied single-celled eukaryote model organism for cellular and molecular biology. However, the lack of extensive T. thermophila cDNA libraries or a large expressed sequence tag (EST) database limited the quality of the original genome annotation. Methodology/Principal Findings This RNA-seq study describes the first deep sequencing analysis … Continue readingResearch Summary: Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing

Research Summary: NF90 Binds the Dengue Virus RNA 3′ Terminus and Is a Positive Regulator of Dengue Virus Replication

 

ABSTRACT Background Viral RNA translation and replication are regulated by sequence and structural elements in the 5′ and 3′ untranslated regions (UTR) and by host cell and/or viral proteins that bind them. Dengue virus has a single-stranded RNA genome with positive polarity, a 5′ m7GpppG cap, and a conserved 3′-terminal stem loop (SL) that is … Continue readingResearch Summary: NF90 Binds the Dengue Virus RNA 3′ Terminus and Is a Positive Regulator of Dengue Virus Replication

Research Summary: Aberrant Herpesvirus-Induced Polyadenylation Correlates With Cellular Messenger RNA Destruction

 

Abstract Inhibition of host cell gene expression by the human herpesvirus KSHV occurs via a novel mechanism involving polyadenylation-linked RNA turnover. ____________________________ Publisher: Public Library of Science Author(s): Lee Y., Glaunsinger B. Link: https://doi.org/10.1371/journal.pbio.1000107

Research Summary: Adaptation of A-to-I RNA editing in Drosophila

 

ABSTRACT Adenosine-to-inosine (A-to-I) editing is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach. However, it is challenging to provide evidences to support this hypothesis at the whole editome level. In this study, we systematically characterized 2,114 A-to-I RNA editing sites in female and male brains of D. melanogaster, and nearly … Continue readingResearch Summary: Adaptation of A-to-I RNA editing in Drosophila

Research Summary: Clusters of Basic Amino Acids Contribute to RNA Binding and Nucleolar Localization of Ribosomal Protein L22

 

ABSTRACT The ribosomal protein L22 is a component of the 60S eukaryotic ribosomal subunit. As an RNA-binding protein, it has been shown to interact with both cellular and viral RNAs including 28S rRNA and the Epstein-Barr virus encoded RNA, EBER-1. L22 is localized to the cell nucleus where it accumulates in nucleoli. Although previous studies … Continue readingResearch Summary: Clusters of Basic Amino Acids Contribute to RNA Binding and Nucleolar Localization of Ribosomal Protein L22

Research Summary: Xist Exon 7 Contributes to the Stable Localization of Xist RNA on the Inactive X-Chromosome

 

ABSTRACT To equalize X-linked gene dosage between the sexes in mammalian females, Xist RNA inactivates one of the two X-chromosomes. Here, we report the crucial function of Xist exon 7 in X-inactivation. Xist exon 7 is the second-largest exon with a well-conserved repeat E in eutherian mammals, but its role is often overlooked in X-inactivation. … Continue readingResearch Summary: Xist Exon 7 Contributes to the Stable Localization of Xist RNA on the Inactive X-Chromosome

Research Summary: Genome-Wide Identification of Small RNAs in the Opportunistic Pathogen Enterococcus faecalis V583

 

ABSTRACT Small RNA molecules (sRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sRNAs in the Gram positive opportunistic pathogen Enterococcus faecalis. We characterized 11 sRNAs by tiling microarray analysis, 5′ and 3′ RACE-PCR, and Northern blot analysis. Six sRNAs were specifically expressed at exponential … Continue readingResearch Summary: Genome-Wide Identification of Small RNAs in the Opportunistic Pathogen Enterococcus faecalis V583

Research Summary: T7 RNA Polymerase Functions In Vitro without Clustering

 

ABSTRACT Many nucleic acid polymerases function in clusters known as factories. We investigate whether the RNA polymerase (RNAP) of phage T7 also clusters when active. Using ‘pulldowns’ and fluorescence correlation spectroscopy we find that elongation complexes do not interact in vitro with a Kd<1 µM. Chromosome conformation capture also reveals that genes located 100 kb … Continue readingResearch Summary: T7 RNA Polymerase Functions In Vitro without Clustering

Research Summary: The RNA-Binding Protein QKI Suppresses Cancer-Associated Aberrant Splicing

 

Abstract Lung cancer is the leading cause of cancer-related death worldwide. Aberrant splicing has been implicated in lung tumorigenesis. However, the functional links between splicing regulation and lung cancer are not well understood. Here we identify the RNA-binding protein QKI as a key regulator of alternative splicing in lung cancer. We show that QKI is … Continue readingResearch Summary: The RNA-Binding Protein QKI Suppresses Cancer-Associated Aberrant Splicing

Research Summary: Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

 

ABSTRACT Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical … Continue readingResearch Summary: Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

Research Summary: The LARK RNA-Binding Protein Selectively Regulates the Circadian Eclosion Rhythm by Controlling E74 Protein Expression

 

ABSTRACT Despite substantial progress in defining central components of the circadian pacemaker, the output pathways coupling the clock to rhythmic physiological events remain elusive. We previously showed that LARK is a Drosophila RNA-binding protein which functions downstream of the clock to mediate behavioral outputs. To better understand the roles of LARK in the circadian system, … Continue readingResearch Summary: The LARK RNA-Binding Protein Selectively Regulates the Circadian Eclosion Rhythm by Controlling E74 Protein Expression

Research Summary: Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

 

ABSTRACT RNA biomarkers discovered by RT-PCR-based gene expression profiling of archival formalin-fixed paraffin-embedded (FFPE) tissue form the basis for widely used clinical diagnostic tests; however, RT-PCR is practically constrained in the number of transcripts that can be interrogated. We have developed and optimized RNA-Seq library chemistry as well as bioinformatics and biostatistical methods for whole … Continue readingResearch Summary: Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

Research Summary: Protocol for Nearly Full-Length Sequencing of HIV-1 RNA from Plasma

 

ABSTRACT Nearly full-length genome sequencing of HIV-1 using peripheral blood mononuclear cells (PBMC) DNA as a template for PCR is now a relatively routine laboratory procedure. However, this has not been the case when using virion RNA as the template and this has made full genome analysis of circulating viruses difficult. Therefore, a well-developed procedure … Continue readingResearch Summary: Protocol for Nearly Full-Length Sequencing of HIV-1 RNA from Plasma

Research Summary: An “In-Depth” Description of the Small Non-coding RNA Population of Schistosoma japonicum Schistosomulum

 

ABSTRACT Parasitic flatworms of the genus Schistosoma are the causative agents of schistosomiasis, which afflicts more than 200 million people yearly in tropical regions of South America, Asia and Africa. A promising approach to the control of this and many other diseases involves the application of our understanding of small non-coding RNA function to the … Continue readingResearch Summary: An “In-Depth” Description of the Small Non-coding RNA Population of Schistosoma japonicum Schistosomulum

Research Summary: Identification and Characterization of Argonaute Protein, Ago2 and Its Associated Small RNAs in Schistosoma japonicum

 

ABSTRACT Background The complex life cycle of the genus Schistosoma drives the parasites to employ subtle developmentally dependent gene regulatory machineries. Small non-coding RNAs (sncRNAs) are essential gene regulatory factors that, through their impact on mRNA and genome stability, control stage-specific gene expression. Abundant sncRNAs have been identified in this genus. However, their functionally associated … Continue readingResearch Summary: Identification and Characterization of Argonaute Protein, Ago2 and Its Associated Small RNAs in Schistosoma japonicum

Research Summary: Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

 

Abstract Tinkering with pre-existing genes has long been known as a major way to create new genes. Recently, however, motherless protein-coding genes have been found to have emerged de novo from ancestral non-coding DNAs. How these genes originated is not well addressed to date. Here we identified 24 hominoid-specific de novo protein-coding genes with precise … Continue readingResearch Summary: Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

Research Summary: The meiotic phosphatase GSP-2/PP1 promotes germline immortality and small RNA-mediated genome silencing

 

ABSTRACT Germ cell immortality, or transgenerational maintenance of the germ line, could be promoted by mechanisms that could occur in either mitotic or meiotic germ cells. Here we report for the first time that the GSP-2 PP1/Glc7 phosphatase promotes germ cell immortality. Small RNA-induced genome silencing is known to promote germ cell immortality, and we … Continue readingResearch Summary: The meiotic phosphatase GSP-2/PP1 promotes germline immortality and small RNA-mediated genome silencing

Research Summary: The Putative RNA Helicase HELZ Promotes Cell Proliferation, Translation Initiation and Ribosomal Protein S6 Phosphorylation

 

ABSTRACT The hypoxia–inducible transcription factor (HIF) is a key component of the cellular adaptation mechanisms to hypoxic conditions. HIFα subunits are degraded by prolyl-4-hydroxylase domain (PHD) enzyme-dependent prolyl-4-hydroxylation of LxxLAP motifs that confer oxygen-dependent proteolytic degradation. Interestingly, only three non-HIFα proteins contain two conserved LxxLAP motifs, including the putative RNA helicase with a zinc finger … Continue readingResearch Summary: The Putative RNA Helicase HELZ Promotes Cell Proliferation, Translation Initiation and Ribosomal Protein S6 Phosphorylation

Research Summary: A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B

 

ABSTRACT The replacement of histone H2A with its variant forms is critical for regulating all aspects of genome organisation and function. The histone variant H2A.B appeared late in evolution and is most highly expressed in the testis followed by the brain in mammals. This raises the question of what new function(s) H2A.B might impart to … Continue readingResearch Summary: A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B

Research Summary: Inhibition of Dengue Virus Entry and Multiplication into Monocytes Using RNA Interference

 

ABSTRACT Background Dengue infection ranks as one of the most significant viral diseases of the globe. Currently, there is no specific vaccine or antiviral therapy for prevention or treatment. Monocytes/macrophages are the principal target cells for dengue virus and are responsible for disseminating the virus after its transmission. Dengue virus enters target cells via receptor-mediated … Continue readingResearch Summary: Inhibition of Dengue Virus Entry and Multiplication into Monocytes Using RNA Interference

Research Summary: Re-Inspection of Small RNA Sequence Datasets Reveals Several Novel Human miRNA Genes

 

ABSTRACT Background miRNAs are key players in gene expression regulation. To fully understand the complex nature of cellular differentiation or initiation and progression of disease, it is important to assess the expression patterns of as many miRNAs as possible. Thereby, identifying novel miRNAs is an essential prerequisite to make possible a comprehensive and coherent understanding … Continue readingResearch Summary: Re-Inspection of Small RNA Sequence Datasets Reveals Several Novel Human miRNA Genes

Research Summary: Emergence of a Code in the Polymerization of Amino Acids along RNA Templates

 

ABSTRACT The origin of the genetic code in the context of an RNA world is a major problem in the field of biophysical chemistry. In this paper, we describe how the polymerization of amino acids along RNA templates can be affected by the properties of both molecules. Considering a system without enzymes, in which the … Continue readingResearch Summary: Emergence of a Code in the Polymerization of Amino Acids along RNA Templates

Research Summary: sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

 

ABSTRACT Background Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings Here we have proposed a transcriptional signal-based … Continue readingResearch Summary: sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Research Summary: Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

 

Abstract Protein-RNA docking is hampered by the high flexibility of RNA, and particularly single-stranded RNA (ssRNA). Yet, ssRNA regions typically carry the specificity of protein recognition. The lack of methodology for modeling such regions limits the accuracy of current protein-RNA docking methods. We developed a fragment-based approach to model protein-bound ssRNA, based on the structure … Continue readingResearch Summary: Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

Research Summary: Anti- Japanese-Encephalitis-Viral Effects of Kaempferol and Daidzin and Their RNA-Binding Characteristics

 

ABSTRACT Background New therapeutic tools and molecular targets are needed for treatment of Japanese encephalitis virus (JEV) infections. JEV requires an α-1 translational frameshift to synthesize the NS1′ protein required for viral neuroinvasiveness. Several flavonoids have been shown to possess antiviral activity in vitro against a wide spectrum of viruses. To date, the antiviral activities … Continue readingResearch Summary: Anti- Japanese-Encephalitis-Viral Effects of Kaempferol and Daidzin and Their RNA-Binding Characteristics

Research Summary: RNA Binding Protein CUGBP2/CELF2 Mediates Curcumin-Induced Mitotic Catastrophe of Pancreatic Cancer Cells

 

ABSTRACT Background Curcumin inhibits the growth of pancreatic cancer tumor xenografts in nude mice; however, the mechanism of action is not well understood. It is becoming increasingly clear that RNA binding proteins regulate posttranscriptional gene expression and play a critical role in RNA stability and translation. Here, we have determined that curcumin modulates the expression … Continue readingResearch Summary: RNA Binding Protein CUGBP2/CELF2 Mediates Curcumin-Induced Mitotic Catastrophe of Pancreatic Cancer Cells

Research Summary: The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA–Dependent RNA Polymerases

 

Abstract Tomato Yellow Leaf Curl Virus Disease incited by Tomato yellow leaf curl virus (TYLCV) causes huge losses in tomato production worldwide and is caused by different related begomovirus species. Breeding for TYLCV resistance has been based on the introgression of multiple resistance genes originating from several wild tomato species. In this study we have … Continue readingResearch Summary: The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA–Dependent RNA Polymerases

Research Summary: The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage

 

ABSTRACT RNA-DNA hybrids are naturally occurring obstacles that must be overcome by the DNA replication machinery. In the absence of RNase H enzymes, RNA-DNA hybrids accumulate, resulting in replication stress, DNA damage and compromised genomic integrity. We demonstrate that Mph1, the yeast homolog of Fanconi anemia protein M (FANCM), is required for cell viability in … Continue readingResearch Summary: The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage

Research Summary: Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

 

Abstract The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers. However, the specificity of the response across stimuli and cell types, and the roles of non-coding RNAs are not well understood. Using a large collection of densely-sampled time series expression data we have examined … Continue readingResearch Summary: Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

Research Summary: RNA-Seq vs Dual- and Single-Channel Microarray Data: Sensitivity Analysis for Differential Expression and Clustering

 

ABSTRACT With the fast development of high-throughput sequencing technologies, a new generation of genome-wide gene expression measurements is under way. This is based on mRNA sequencing (RNA-seq), which complements the already mature technology of microarrays, and is expected to overcome some of the latter’s disadvantages. These RNA-seq data pose new challenges, however, as strengths and … Continue readingResearch Summary: RNA-Seq vs Dual- and Single-Channel Microarray Data: Sensitivity Analysis for Differential Expression and Clustering

Research Summary: The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice

 

ABSTRACT N6-Methyladenosine (m6A) RNA methylation plays important roles during development in different species. However, knowledge of m6A RNA methylation in monocots remains limited. In this study, we reported that OsFIP and OsMTA2 are the components of m6A RNA methyltransferase complex in rice and uncovered a previously unknown function of m6A RNA methylation in regulation of … Continue readingResearch Summary: The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice

Research Summary: Alu Sequences in Undifferentiated Human Embryonic Stem Cells Display High Levels of A-to-I RNA Editing

 

ABSTRACT Adenosine to Inosine (A-to-I) RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA) protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, … Continue readingResearch Summary: Alu Sequences in Undifferentiated Human Embryonic Stem Cells Display High Levels of A-to-I RNA Editing

Research Summary: Repeat Length and RNA Expression Level Are Not Primary Determinants in CUG Expansion Toxicity in Drosophila Models

 

ABSTRACT Evidence for an RNA gain-of-function toxicity has now been provided for an increasing number of human pathologies. Myotonic dystrophies (DM) belong to a class of RNA-dominant diseases that result from RNA repeat expansion toxicity. Specifically, DM of type 1 (DM1), is caused by an expansion of CUG repeats in the 3′UTR of the DMPK … Continue readingResearch Summary: Repeat Length and RNA Expression Level Are Not Primary Determinants in CUG Expansion Toxicity in Drosophila Models

Research Summary: Analysis of the Tomato spotted wilt virus Ambisense S RNA-Encoded Hairpin Structure in Translation

 

ABSTRACT Background The intergenic region (IR) of ambisense RNA segments from animal- and plant-infecting (-)RNA viruses functions as a bidirectional transcription terminator. The IR sequence of the Tomato spotted wilt virus (TSWV) ambisense S RNA contains stretches that are highly rich in A-residues and U-residues and is predicted to fold into a stable hairpin structure. … Continue readingResearch Summary: Analysis of the Tomato spotted wilt virus Ambisense S RNA-Encoded Hairpin Structure in Translation

Research Summary: Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

 

ABSTRACT C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across … Continue readingResearch Summary: Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

Research Summary: RNA-Processing Protein TDP-43 Regulates FOXO-Dependent Protein Quality Control in Stress Response

 

ABSTRACT Protein homeostasis is critical for cell survival and functions during stress and is regulated at both RNA and protein levels. However, how the cell integrates RNA-processing programs with post-translational protein quality control systems is unknown. Transactive response DNA-binding protein (TARDBP/TDP-43) is an RNA-processing protein that is involved in the pathogenesis of major neurodegenerative diseases, … Continue readingResearch Summary: RNA-Processing Protein TDP-43 Regulates FOXO-Dependent Protein Quality Control in Stress Response

Research Summary: The Infectious Bursal Disease Virus RNA-Binding VP3 Polypeptide Inhibits PKR-Mediated Apoptosis

 

ABSTRACT Infectious bursal disease virus (IBDV) is an avian pathogen responsible for an acute immunosuppressive disease that causes major losses to the poultry industry. Despite having a bipartite dsRNA genome, IBDV, as well as other members of the Birnaviridae family, possesses a single capsid layer formed by trimers of the VP2 capsid protein. The capsid … Continue readingResearch Summary: The Infectious Bursal Disease Virus RNA-Binding VP3 Polypeptide Inhibits PKR-Mediated Apoptosis

Research Summary: PanoView: An iterative clustering method for single-cell RNA sequencing data

 

Abstract Single-cell RNA-sequencing (scRNA-seq) provides new opportunities to gain a mechanistic understanding of many biological processes. Current approaches for single cell clustering are often sensitive to the input parameters and have difficulty dealing with cell types with different densities. Here, we present Panoramic View (PanoView), an iterative method integrated with a novel density-based clustering, Ordering … Continue readingResearch Summary: PanoView: An iterative clustering method for single-cell RNA sequencing data

Research Summary: Small Molecule Amiloride Modulates Oncogenic RNA Alternative Splicing to Devitalize Human Cancer Cells

 

ABSTRACT Alternative splicing involves differential exon selection of a gene transcript to generate mRNA and protein isoforms with structural and functional diversity. Abnormal alternative splicing has been shown to be associated with malignant phenotypes of cancer cells, such as chemo-resistance and invasive activity. Screening small molecules and drugs for modulating RNA splicing in human hepatocellular … Continue readingResearch Summary: Small Molecule Amiloride Modulates Oncogenic RNA Alternative Splicing to Devitalize Human Cancer Cells

Research Summary: Profiles of Small Non-Coding RNAs in Schistosoma japonicum during Development

 

ABSTRACT Background The gene regulation mechanism along the life cycle of the genus Schistosoma is complex. Small non-coding RNAs (sncRNAs) are essential post transcriptional gene regulation elements that affect gene expression and mRNA stability. Preliminary studies indicated that sncRNAs in schistosomal parasites are generated through different pathways, which are developmentally regulated. However, the data of … Continue readingResearch Summary: Profiles of Small Non-Coding RNAs in Schistosoma japonicum during Development

Research Summary: The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus

 

Abstract Prochlorococcus, an extremely small cyanobacterium that is very abundant in the world’s oceans, has a very streamlined genome. On average, these cells have about 2,000 genes and very few regulatory proteins. The limited capability of regulation is thought to be a result of selection imposed by a relatively stable environment in combination with a … Continue readingResearch Summary: The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus

Research Summary: RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

 

Abstract Metazoan genomes encode hundreds of RNA-binding proteins (RBPs). These proteins regulate post-transcriptional gene expression and have critical roles in numerous cellular processes including mRNA splicing, export, stability and translation. Despite their ubiquity and importance, the binding preferences for most RBPs are not well characterized. In vitro and in vivo studies, using affinity selection-based approaches, … Continue readingResearch Summary: RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

Research Summary: Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

 

Abstract CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of … Continue readingResearch Summary: Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

Research Summary: Co-translational Localization of an LTR-Retrotransposon RNA to the Endoplasmic Reticulum Nucleates Virus-Like Particle Assembly Sites

 

Abstract The transcript of retrovirus-like transposons functions as an mRNA for synthesis of capsid and replication proteins and as the genomic RNA of virus-like particles (VLPs), wherein the genome is replicated. Retrotransposon RNA and proteins coalesce in a cytoplasmic focus, or retrosome, to initiate VLP assembly, but it is not known how the retrosome is … Continue readingResearch Summary: Co-translational Localization of an LTR-Retrotransposon RNA to the Endoplasmic Reticulum Nucleates Virus-Like Particle Assembly Sites

Research Summary: A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

 

ABSTRACT Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification … Continue readingResearch Summary: A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

Research Summary: Fragile Mental Retardation Protein Interacts with the RNA-Binding Protein Caprin1 in Neuronal RiboNucleoProtein Complexes

 

ABSTRACT Fragile X syndrome is caused by the absence of the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein. FMRP is associated with messenger RiboNucleoParticles (mRNPs) present in polyribosomes and its absence in neurons leads to alteration in synaptic plasticity as a result of translation regulation defects. The molecular mechanisms by which FMRP plays … Continue readingResearch Summary: Fragile Mental Retardation Protein Interacts with the RNA-Binding Protein Caprin1 in Neuronal RiboNucleoProtein Complexes

Research Summary: Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

 

Abstract The epigenetic activity of transposable elements (TEs) can influence the regulation of genes; though, this regulation is confined to the genes, promoters, and enhancers that neighbor the TE. This local cis regulation of genes therefore limits the influence of the TE’s epigenetic regulation on the genome. TE activity is suppressed by small RNAs, which … Continue readingResearch Summary: Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

Research Summary: A Pre-mRNA-Splicing Factor Is Required for RNA-Directed DNA Methylation in Arabidopsis

 

Abstract Cytosine DNA methylation is a stable epigenetic mark that is frequently associated with the silencing of genes and transposable elements (TEs). In Arabidopsis, the establishment of DNA methylation is through the RNA-directed DNA methylation (RdDM) pathway. Here, we report the identification and characterization of RDM16, a new factor in the RdDM pathway. Mutation of … Continue readingResearch Summary: A Pre-mRNA-Splicing Factor Is Required for RNA-Directed DNA Methylation in Arabidopsis

Research Summary: Artificial Hybrids of Influenza A Virus RNA Polymerase Reveal PA Subunit Modulates Its Thermal Sensitivity

 

ABSTRACT Background Influenza A virus can infect a variety of different hosts and therefore has to adapt to different host temperatures for its efficient viral replication. Influenza virus codes for an RNA polymerase of 3 subunits: PB1, PB2 and PA. It is well known that the PB2 subunit is involved in temperature sensitivity, such as … Continue readingResearch Summary: Artificial Hybrids of Influenza A Virus RNA Polymerase Reveal PA Subunit Modulates Its Thermal Sensitivity

Research Summary: A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing

 

ABSTRACT C-to-U editing of transcripts in plant organelles is carried out by small (<400 kD) protein complexes called editosomes. Recognition of the proper C target for editing is mediated by pentatricopeptide repeat (PPR) containing proteins that recognize cis-elements. Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be … Continue readingResearch Summary: A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing

Research Summary: Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells

 

ABSTRACT Genes or their encoded products are not expected to mingle with each other unless in some disease situations. In cancer, a frequent mechanism that can produce gene fusions is chromosomal rearrangement. However, recent discoveries of RNA trans-splicing and cis-splicing between adjacent genes (cis-SAGe) support for other mechanisms in generating fusion RNAs. In our transcriptome … Continue readingResearch Summary: Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells

Research Abstract: iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

 

Abstract Transcriptome-wide analysis of protein-RNA interactions predicts the dual splicing effects of TIA proteins, showing that their local enhancing function is associated with diverse distal splicing silencing effects. ____________________________ Publisher: Public Library of Science Date Published: 26-October-2010 Author(s): Wang Z., Kayikci M., Briese M., Zarnack K., Luscombe N., Rot G., Zupan B., Curk T., Ule … Continue readingResearch Abstract: iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Research Summary: Molecular Dynamics Studies of the Nucleoprotein of Influenza A Virus: Role of the Protein Flexibility in RNA Binding

 

ABSTRACT The influenza viruses contain a segmented, negative stranded RNA genome. Each RNA segment is covered by multiple copies of the nucleoprotein (NP). X-ray structures have shown that NP contains well-structured domains juxtaposed with regions of missing electron densities corresponding to loops. In this study, we tested if these flexible loops gated or promoted RNA … Continue readingResearch Summary: Molecular Dynamics Studies of the Nucleoprotein of Influenza A Virus: Role of the Protein Flexibility in RNA Binding

Research Summary: The Yeast Rab GTPase Ypt1 Modulates Unfolded Protein Response Dynamics by Regulating the Stability of HAC1 RNA

 

Abstract The unfolded protein response (UPR) is a conserved mechanism that mitigates accumulation of unfolded proteins in the ER. The yeast UPR is subject to intricate post-transcriptional regulation, involving recruitment of the RNA encoding the Hac1 transcription factor to the ER and its unconventional splicing. To investigate the mechanisms underlying regulation of the UPR, we … Continue readingResearch Summary: The Yeast Rab GTPase Ypt1 Modulates Unfolded Protein Response Dynamics by Regulating the Stability of HAC1 RNA

Research Summary: High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop

 

ABSTRACT The active sites of multisubunit RNA polymerases have a “trigger loop” (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various … Continue readingResearch Summary: High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop

Research Summary: Quantitative Analysis of Focused A-To-I RNA Editing Sites by Ultra-High-Throughput Sequencing in Psychiatric Disorders

 

ABSTRACT A-to-I RNA editing is a post-transcriptional modification of single nucleotides in RNA by adenosine deamination, which thereby diversifies the gene products encoded in the genome. Thousands of potential RNA editing sites have been identified by recent studies (e.g. see Li et al, Science 2009); however, only a handful of these sites have been independently … Continue readingResearch Summary: Quantitative Analysis of Focused A-To-I RNA Editing Sites by Ultra-High-Throughput Sequencing in Psychiatric Disorders

Research Summary: High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

 

Abstract Replication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone … Continue readingResearch Summary: High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

Research Summary: Expression of IMP1 Enhances Production of Murine Leukemia Virus Vector by Facilitating Viral Genomic RNA Packaging

 

ABSTRACT Murine leukemia virus (MLV)-based retroviral vector is widely used for gene transfer. Efficient packaging of the genomic RNA is critical for production of high-titer virus. Here, we report that expression of the insulin-like growth factor II mRNA binding protein 1 (IMP1) enhanced the production of infectious MLV vector. Overexpression of IMP1 increased the stability … Continue readingResearch Summary: Expression of IMP1 Enhances Production of Murine Leukemia Virus Vector by Facilitating Viral Genomic RNA Packaging

Research Summary: H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions

 

Abstract Extremely AT-rich DNA sequences present a challenging template for specific recognition by RNA polymerase. In bacteria, this is because the promoter −10 hexamer, the major DNA element recognised by RNA polymerase, is itself AT-rich. We show that Histone-like Nucleoid Structuring (H-NS) protein can facilitate correct recognition of a promoter by RNA polymerase in AT-rich … Continue readingResearch Summary: H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions

Research Summary: The small non-coding RNA response to virus infection in the Leishmania vector Lutzomyia longipalpis

 

ABSTRACT Sandflies are well known vectors for Leishmania but also transmit a number of arthropod-borne viruses (arboviruses). Few studies have addressed the interaction between sandflies and arboviruses. RNA interference (RNAi) mechanisms utilize small non-coding RNAs to regulate different aspects of host-pathogen interactions. The small interfering RNA (siRNA) pathway is a broad antiviral mechanism in insects. … Continue readingResearch Summary: The small non-coding RNA response to virus infection in the Leishmania vector Lutzomyia longipalpis

Research Summary: Solving the RNA design problem with reinforcement learning

 

Abstract We use reinforcement learning to train an agent for computational RNA design: given a target secondary structure, design a sequence that folds to that structure in silico. Our agent uses a novel graph convolutional architecture allowing a single model to be applied to arbitrary target structures of any length. After training it on randomly … Continue readingResearch Summary: Solving the RNA design problem with reinforcement learning

Research Summary: Exosomes Communicate Protective Messages during Oxidative Stress; Possible Role of Exosomal Shuttle RNA

 

ABSTRACT Background Exosomes are small extracellular nanovesicles of endocytic origin that mediate different signals between cells, by surface interactions and by shuttling functional RNA from one cell to another. Exosomes are released by many cells including mast cells, dendritic cells, macrophages, epithelial cells and tumour cells. Exosomes differ compared to their donor cells, not only … Continue readingResearch Summary: Exosomes Communicate Protective Messages during Oxidative Stress; Possible Role of Exosomal Shuttle RNA

Research Summary: New Small Nuclear RNA Gene-Like Transcriptional Units as Sources of Regulatory Transcripts

 

Abstract By means of a computer search for upstream promoter elements (distal sequence element and proximal sequence element) typical of small nuclear RNA genes, we have identified in the human genome a number of previously unrecognized, putative transcription units whose predicted products are novel noncoding RNAs with homology to protein-coding genes. By elucidating the function … Continue readingResearch Summary: New Small Nuclear RNA Gene-Like Transcriptional Units as Sources of Regulatory Transcripts

Research Summary: Depolarization and CaM Kinase IV Modulate NMDA Receptor Splicing through Two Essential RNA Elements

 

Abstract Alternative splicing controls the activity of many proteins important for neuronal excitation, but the signal-transduction pathways that affect spliced isoform expression are not well understood. One particularly interesting system of alternative splicing is exon 21 (E21) of the NMDA receptor 1 (NMDAR1 E21), which controls the trafficking of NMDA receptors to the plasma membrane … Continue readingResearch Summary: Depolarization and CaM Kinase IV Modulate NMDA Receptor Splicing through Two Essential RNA Elements

Research Summary: Metagenomic Analysis of RNA Viruses in a Fresh Water Lake

 

ABSTRACT Freshwater lakes and ponds present an ecological interface between humans and a variety of host organisms. They are a habitat for the larval stage of many insects and may serve as a medium for intraspecies and interspecies transmission of viruses such as avian influenza A virus. Furthermore, freshwater bodies are already known repositories for … Continue readingResearch Summary: Metagenomic Analysis of RNA Viruses in a Fresh Water Lake

Research Summary: Regulation of Small RNA Accumulation in the Maize Shoot Apex

 

Abstract MicroRNAs (miRNAs) and trans-acting siRNAs (ta-siRNAs) are essential to the establishment of adaxial–abaxial (dorsoventral) leaf polarity. Tas3-derived ta-siRNAs define the adaxial side of the leaf by restricting the expression domain of miRNA miR166, which in turn demarcates the abaxial side of leaves by restricting the expression of adaxial determinants. To investigate the regulatory mechanisms … Continue readingResearch Summary: Regulation of Small RNA Accumulation in the Maize Shoot Apex

Research Summary: Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq

 

Abstract Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages (A-H). Only assemblages A and B infect humans and are suggested to represent two different Giardia species. Correlations exist between assemblage type and host-specificity and to some extent symptoms. Phenotypical differences have been documented between … Continue readingResearch Summary: Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq

Research Summary: Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism

 

Abstract Abortive infection, during which an infected bacterial cell commits altruistic suicide to destroy the replicating bacteriophage and protect the clonal population, can be mediated by toxin-antitoxin systems such as the Type III protein–RNA toxin-antitoxin system, ToxIN. A flagellum-dependent bacteriophage of the Myoviridae, ΦTE, evolved rare mutants that “escaped” ToxIN-mediated abortive infection within Pectobacterium atrosepticum. … Continue readingResearch Summary: Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism

Research Summary: Structural and Biochemical Studies on ATP Binding and Hydrolysis by the Escherichia coli RNA Chaperone Hfq

 

ABSTRACT In Escherichia coli the RNA chaperone Hfq is involved in riboregulation by assisting base-pairing between small regulatory RNAs (sRNAs) and mRNA targets. Several structural and biochemical studies revealed RNA binding sites on either surface of the donut shaped Hfq-hexamer. Whereas sRNAs are believed to contact preferentially the YKH motifs present on the proximal site, … Continue readingResearch Summary: Structural and Biochemical Studies on ATP Binding and Hydrolysis by the Escherichia coli RNA Chaperone Hfq

Research Summary: A Cell-Based Method for Screening RNA-Protein Interactions: Identification of Constitutive Transport Element-Interacting Proteins

 

ABSTRACT We have developed a mammalian cell-based screening platform to identify proteins that assemble into RNA-protein complexes. Based on Tat-mediated activation of the HIV LTR, proteins that interact with an RNA target elicit expression of a GFP reporter and are captured by fluorescence activated cell sorting. This “Tat-hybrid” screening platform was used to identify proteins … Continue readingResearch Summary: A Cell-Based Method for Screening RNA-Protein Interactions: Identification of Constitutive Transport Element-Interacting Proteins

Research Summary: Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

 

Abstract A large proportion of functional sequence within mammalian genomes falls outside protein-coding exons and can be transcribed into long RNAs. However, the roles in mammalian biology of long noncoding RNA (lncRNA) are not well understood. Few lncRNAs have experimentally determined roles, with some of these being lineage-specific. Determining the extent by which transcription of … Continue readingResearch Summary: Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

Research Summary: deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

 

Abstract Gene fusions created by somatic genomic rearrangements are known to play an important role in the onset and development of some cancers, such as lymphomas and sarcomas. RNA-Seq (whole transcriptome shotgun sequencing) is proving to be a useful tool for the discovery of novel gene fusions in cancer transcriptomes. However, algorithmic methods for the … Continue readingResearch Summary: deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

Research Summary: Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

 

Abstract It has become clear that noncoding RNAs (ncRNA) play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist computational methods that can be used to search for ncRNAs by comparing sequences from different genomes. One main problem with these methods … Continue readingResearch Summary: Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

Research Summary: Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription

 

ABSTRACT A relationship exists between nuclear architecture and gene activity and it has been proposed that the activity of ongoing RNA polymerase II transcription determines genome organization in the mammalian cell nucleus. Recently developed 3C and 4C technology allowed us to test the importance of transcription for nuclear architecture. We demonstrate that upon transcription inhibition … Continue readingResearch Summary: Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription

Research Abstract: RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis

 

Abstract The structure of a ribosome assembly factor in complex bound to a ribosomal protein uncovers a chaperoning function that uses RNA mimicry and is regulated by ATP hydrolysis. ____________________________ Publisher: Public Library of Science Date Published: 13-May-2014 Author(s): Loc’h J., Blaud M., Réty S., Lebaron S., Deschamps P., Bareille J., Jombart J., Robert-Paganin J., … Continue readingResearch Abstract: RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis

Research Summary: Rescue of Foot-and-Mouth Disease Viruses That Are Pathogenic for Cattle from Preserved Viral RNA Samples

 

ABSTRACT Background Foot and mouth disease is an economically important disease of cloven-hoofed animals including cattle, sheep and pigs. It is caused by a picornavirus, foot-and-mouth disease virus (FMDV), which has a positive sense RNA genome which, when introduced into cells, can initiate virus replication. Principal Findings A system has been developed to rescue infectious … Continue readingResearch Summary: Rescue of Foot-and-Mouth Disease Viruses That Are Pathogenic for Cattle from Preserved Viral RNA Samples

Research Summary: Selective Constraint on Copy Number Variation in Human Piwi-Interacting RNA Loci

 

ABSTRACT Piwi-interacting RNAs (piRNAs) are a recently discovered class of small non-coding RNA found in animals. PiRNAs are primarily expressed in the germline where their best understood function is to repress transposable elements. Unlike previous studies that investigated the evolution of piRNA-generating loci at the level of nucleotide substitutions, here we studied the evolution of … Continue readingResearch Summary: Selective Constraint on Copy Number Variation in Human Piwi-Interacting RNA Loci

Research Summary: Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast

 

Abstract Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes, few of these proteins have been studied systematically. We have used an affinity tag to isolate each of the five members of the Puf family of … Continue readingResearch Summary: Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast

Research Summary: An RNA Polymerase III-Dependent Heterochromatin Barrier at Fission Yeast Centromere 1

 

ABSTRACT Heterochromatin formation involves the nucleation and spreading of structural and epigenetic features along the chromatin fiber. Chromatin barriers and associated proteins counteract the spreading of heterochromatin, thereby restricting it to specific regions of the genome. We have performed gene expression studies and chromatin immunoprecipitation on strains in which native centromere sequences have been mutated … Continue reading