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https://www.readbyqxmd.com/read/28336542/seten-a-tool-for-systematic-identification-and-comparison-of-processes-phenotypes-and-diseases-associated-with-rna-binding-proteins-from-condition-specific-clip-seq-profiles
#1
Gungor Budak, Rajneesh Srivastava, Sarath Chandra Janga
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single nucleotide resolution in a cell, currently there are very few tools which can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps...
March 23, 2017: RNA
https://www.readbyqxmd.com/read/28325845/functional-dissection-of-neat1-using-genome-editing-reveals-substantial-localisation-of-the-neat1_1-isoform-outside-paraspeckles
#2
Ruohan Li, Alan R Harvey, Stuart I Hodgetts, Archa H Fox
Large numbers of long non-coding RNAs have been discovered in recent years, but only a few have been characterised. NEAT1 (nuclear paraspeckle assembly transcript 1) is a mammalian long non-coding RNA that is important for the reproductive physiology of mice, cancer development and the formation of subnuclear bodies termed paraspeckles. The two major isoforms of NEAT1 (3.7kb NEAT1_1 and 23kb NEAT1_2 in human) are generated from a common promoter and are produced through the use of alternative transcription termination sites...
March 21, 2017: RNA
https://www.readbyqxmd.com/read/28325844/the-sole-lsm-complex-in-cyanidioschyzon-merolae-associates-with-pre-mrna-splicing-and-mrna-degradation-factors
#3
Kirsten A Reimer, Martha R Stark, Lisbeth Carolina Aguilar, Sierra R Stark, Robert D Burke, Jack Moore, Richard P Fahlman, Calvin K Yip, Haruko Kuroiwa, Marlene Oeffinger, Stephen D Rader
Proteins of the Sm and Sm-like (LSm) families, referred to collectively as (L)Sm proteins, are found in all three domains of life, and are known to promote a variety of RNA processes such as base-pair formation, unwinding, RNA degradation, and RNA stabilization. In eukaryotes, (L)Sm proteins have been studied, inter alia, for their role in pre-mRNA splicing. In many organisms, the LSm proteins form two distinct complexes, one consisting of LSm1-7 that is involved in mRNA degradation in the cytoplasm, and the other consisting of LSm2-8 that binds spliceosomal U6 snRNA in the nucleus...
March 21, 2017: RNA
https://www.readbyqxmd.com/read/28325843/a-biochemical-framework-for-eif4e-dependent-mrna-export-and-nuclear-re-cycling-of-the-export-machinery
#4
Laurent Volpon, Biljana Culjkovic-Kraljacic, Hye Seon Sohn, Alexis Blanchett-Cohen, Michael J Osborne, Katherine L B Borden
The eukaryotic translation initiation factor eIF4E acts in the nuclear export and translation of a subset of mRNAs. Both of these functions contribute to its oncogenic potential. While the biochemical mechanisms that underlie translation are relatively well understood, the molecular basis for eIF4E's role in mRNA export remains largely unexplored. To date over 3000 transcripts, many encoding oncoproteins, were identified as potential nuclear eIF4E export targets. These target RNAs typically contain a ~50 nucleotide eIF4E sensitivity element (4ESE) in the 3' UTR and a 7-methylguanosine cap on the 5' end...
March 21, 2017: RNA
https://www.readbyqxmd.com/read/28289156/u7-snrnp-is-recruited-to-histone-pre-mrna-in-a-flash-dependent-manner-by-two-separate-regions-of-the-stem-loop-binding-protein
#5
Aleksandra Skrajna, Xiao-Cui Yang, Katarzyna Bucholc, Jun Zhang, Traci M Hall, Michał Dadlez, William F Marzluff, Zbigniew Dominski
Cleavage of histone pre-mRNAs at the 3' end requires Stem-Loop Binding Protein (SLBP) and U7 snRNP that consists of U7 snRNA and a unique Sm ring containing two U7-specific proteins: Lsm10 and Lsm11. Lsm11 interacts with FLASH and together they bring a subset of polyadenylation factors to U7 snRNP, including the CPSF73 endonuclease that cleaves histone pre-mRNA. SLBP binds to a conserved stem-loop structure upstream of the cleavage site and acts by promoting an interaction between the U7 snRNP and a sequence element located downstream of the cleavage site...
March 13, 2017: RNA
https://www.readbyqxmd.com/read/28289155/comprehensive-processing-of-high-throughput-small-rna-sequencing-data-including-quality-checking-normalization-and-differential-expression-analysis-using-the-uea-srna-workbench
#6
Matthew L Beckers, Irina Mohorianu, Matthew B Stocks, Christopher Applegate, Tamas Dalmay, Vincent Moulton
Recently High Throughput Sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20-25 nt non-coding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved...
March 13, 2017: RNA
https://www.readbyqxmd.com/read/28258160/a-new-cis-acting-motif-is-required-for-the-axonal-smn-dependent-anxa2-mrna-localization
#7
Khalil Rihan, Etienne Antoine, Thomas Maurin, Barbara Bardoni, Rémy Bordonné, Johann Soret, Florence Rage
Spinal muscular atrophy (SMA) is caused by mutations and/or deletions of the survival motor neuron gene (SMN1). Besides its function in the biogenesis of spliceosomal snRNPs, SMN might possess a motor neuron specific role and could function in the transport of axonal mRNAs and in the modulation of local protein translation. Accordingly, SMN colocalizes with axonal mRNAs of differentiated NSC-34 motor neuron-like cells. We recently showed that SMN depletion gives rise to a decrease in the axonal transport of the mRNAs encoding Annexin A2 (Anxa2)...
March 3, 2017: RNA
https://www.readbyqxmd.com/read/28258159/single-cell-transcriptomics-reveals-specific-rna-editing-signatures-in-the-human-brain
#8
Ernesto Picardi, David Stephen Horner, Graziano Pesole
While RNA editing by A-to-I deamination is a requisite for neuronal function in humans, it is under investigated in single cells. Here we fill this gap by analysing RNA editing profiles of single cells from the brain cortex of living human subjects. We show that RNA editing levels per cell are bimodally distributed and distinguish between major brain cell types thus providing new insights into neuronal dynamics.
March 3, 2017: RNA
https://www.readbyqxmd.com/read/28250203/microprocessor-dynamics-shows-co-and-post-transcriptional-processing-of-pri-mirnas
#9
Annita Louloupi, Evgenia Ntini, Julia Liz, Ulf Andersson Ørom
miRNAs are small regulatory RNAs involved in the regulation of translation of target transcripts. miRNA biogenesis is a multi-step process starting with the cleavage of the primary miRNA transcript in the nucleus by the Microprocessor complex. Endogenous processing of pri-miRNAs is challenging to study and the in vivo kinetics of this process is not known. Here, we present a method for determining the processing kinetics of pri-miRNAs within intact cells over time using a pulse-chase approach to label transcribed RNA during 15 minutes and follow the processing within a 1-hour window after labeling with bromouridine...
March 1, 2017: RNA
https://www.readbyqxmd.com/read/28250202/atp-is-dispensable-for-both-mirna-and-smaug-mediated-deadenylation-reactions
#10
Sho Niinuma, Yukihide Tomari
microRNAs (miRNAs) as well as the RNA-binding protein Smaug recruit the CCR4-NOT deadenylase complex for shortening of the poly(A) tail. It has been believed that ATP is required for deadenylation induced by miRNAs or Smaug, based on the fact that the deadenylation reaction is blocked by ATP depletion. However, when isolated, neither of the two deadenylases in the CCR4-NOT complex requires ATP by themselves. Thus, it remains unknown why ATP is required for deadenylation by ribonucleoprotein complexes like miRNAs and Smaug...
March 1, 2017: RNA
https://www.readbyqxmd.com/read/28235843/competitive-folding-of-rna-structures-at-a-termination-antitermination-site
#11
Soraya Ait-Bara, Caroline Clerte, Nathalie Declerck, Emmanuel Margeat
Antitermination is a regulatory process based on the competitive folding of terminator/antiterminator structures that can form in the leader region of nascent transcripts. In the case of the Bacillus subtilis licS gene involved in β-glucosides utilization, the binding of the antitermination protein LicT to a short RNA hairpin (RAT) prevents the formation of an overlapping terminator and thereby allows transcription to proceed. Here, we monitored in vitro the competition between termination and antitermination by combining bulk and single-molecule fluorescence-based assays using labelled RNA oligonucleotide constructs of increasing length that mimic the progressive transcription of the terminator invading the antiterminator hairpin...
February 24, 2017: RNA
https://www.readbyqxmd.com/read/28232389/a-complex-of-arabidopsis-drb-proteins-can-impair-dsrna-processing
#12
Marie-Aude Tschopp, Taichiro Iki, Christopher A Brosnan, Pauline E Jullien, Nathan Pumplin
Small RNAs play an important role in regulating gene expression through transcriptional and post-transcriptional gene silencing. Biogenesis of small RNAs from longer double-stranded (ds)RNA requires the activity of DICER-LIKE ribonucleases (DCLs), which in plants are aided by dsRNA binding proteins (DRBs). To gain insight into this pathway in the model plant Arabidopsis, we searched for interactors of DRB4 by immunoprecipitation followed by mass spectrometry-based finger printing and discovered DRB7.1. This interaction, verified by reciprocal co-immunoprecipitation and bimolecular fluorescence complementation, colocalizes with markers of cytoplasmic siRNA bodies and nuclear dicing bodies...
February 23, 2017: RNA
https://www.readbyqxmd.com/read/28223409/asc1-hel2-and-slh1-couple-translation-arrest-to-nascent-chain-degradation
#13
Cole Stone Sitron, Joseph Hun Park, Onn Brandman
Premature arrest of protein synthesis within the open reading frame elicits a protective response that degrades the incomplete nascent chain. In this response, arrested 80S ribosomes are split into their large and small subunits, allowing assembly of the Ribosome Quality control Complex (RQC), which targets nascent chains for degradation. How the cell recognizes arrested nascent chains among the vast pool of actively translating polypeptides is poorly understood. We systematically examined translation arrest and modification of nascent chains in Saccharomyces cerevisiae to characterize the steps that couple arrest to RQC targeting...
February 21, 2017: RNA
https://www.readbyqxmd.com/read/28223408/inducing-circular-rna-formation-using-the-crispr-endoribonuclease-csy4
#14
Erin K Borchardt, Rita M Meganck, Heather A Vincent, Christopher B Ball, Silvia B V Ramos, Nathaniel J Moorman, William F Marzluff, Aravind Asokan
Circular RNAs (circRNAs) are highly stable, covalently closed RNAs that are regulated in a spatiotemporal manner and whose functions are largely unknown. These molecules have the potential to be incorporated into engineered systems with broad technological implications. Here we describe a switch for inducing backsplicing of an engineered circRNA that relies on the CRISPR endoribonuclease, Csy4, as an activator of circularization. The endoribonuclease activity and 3' end-stabilizing properties of Csy4 are particularly suited for this task...
February 21, 2017: RNA
https://www.readbyqxmd.com/read/28213527/advancing-viral-rna-structure-prediction-measuring-the-thermodynamics-of-pyrimidine-rich-internal-loops
#15
Andy Phan, Katherine Mailey, Jessica Sakai, Xiaobo Gu, Susan J Schroeder
Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased towards small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with more than 6 nucleotides that occur frequently in viral RNA...
February 17, 2017: RNA
https://www.readbyqxmd.com/read/28209633/gene-expression-control-by-bacillus-anthracis-purine-riboswitches
#16
Marion Kirchner, Sabine Schneider
In all kingdoms of life, cellular replication relies on the presence of nucleosides and nucleotides, the building blocks of nucleic acids and the main source of energy. In bacteria, the availability of metabolites sometimes directly regulates the expression of enzymes and proteins involved in purine salvage, biosynthesis and uptake through riboswitches. Riboswitches are located in bacterial mRNAs and can control gene expression by conformational changes in response to ligand binding. We have established an inverse reporter gene system in Bacillus subtilis that allows us to monitor riboswitch-controlled gene expression...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#17
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28202710/practical-data-handling-pipeline-improves-performance-of-qpcr-based-circulating-mirna-measurements
#18
Maurice W J de Ronde, Jan M Ruijter, David Lanfear, Antoni Bayes-Genis, Maayke Kok, Esther Creemers, Yigal M Pinto, Sara-Joan Pinto-Sietsma
BACKGROUND: Since numerous miRNAs have been shown to be present in the circulation, these so-called circulating miRNAs have emerged as potential biomarkers for disease. However, results of qPCR studies on circulating miRNA biomarkers vary greatly and many experiments cannot be reproduced. Missing data in qPCR experiments often occur due to off-target amplification, non-analyzable qPCR curves and discordance between replicates. The low concentration of most miRNAs leads to most, but not all missing data...
February 15, 2017: RNA
https://www.readbyqxmd.com/read/28202709/understanding-in-line-probing-experiments-by-modeling-cleavage-of-non-reactive-rna-nucleotides
#19
Vojtech Mlynsky, Giovanni Bussi
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work we used a combination of theoretical approaches, i...
February 15, 2017: RNA
https://www.readbyqxmd.com/read/28193673/structure-of-the-escherichia-coli-proq-rna-chaperone-protein
#20
Grecia Gonzalez, Steven Hardwick, Sarah L Maslen, J Mark Skehel, Erik Holmqvist, Jörg Vogel, Alex Bateman, Ben Luisi, R William Broadhurst
The protein ProQ has recently been identified as a global RNA chaperone in Salmonella, and a similar role is anticipated for its numerous homologues in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor-domain fold commonly found in eukaryotes, and an elongated bridging intra-domain linker that is flexible but nonetheless incompressible. Structure based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain...
February 13, 2017: RNA
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