Topic 49

mrna translation mrnas rna ribosome rnas transcripts protein splicing regulation translational binding ribosomes ribosomal molecular coding proteins expression conserved biology gene codon genes decay transcriptional degradation initiation termination introns transcript transcription transcriptome biogenesis utr regulate intron codons synthesis regulated function post regulatory functions elongation enriched translated mirna untranslated regulates cytoplasmic profiling nascent splice nuclear mirnas upstream yeast alternative role trna sites mediated spliced sequence pre seq roles machinery expressed exons containing mechanism target levels reading exon depletion utrs site poly identified non targets terminal sequences rrna granules encoding micrornas cellular motif elements abundance silencing show regulating specific polyadenylation control srna

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FMRP Links Optimal Codons to mRNA stability in Neurons 49 3

Functional and structural basis of extreme non-coding conservation in vertebrate mRNAs 134 49 31 9 3

Alteration of the premature tRNA landscape by gammaherpesvirus infection 49 41 31 9 3

Nonsense mediated RNA decay factor UPF1 is critical for post-transcriptional and translational gene regulation in Arabidopsis 49 16 3

TRIBE editing reveals specific mRNA targets of eIF4E-BP in Drosophila and in mammals 49 3

Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential 49 7 3

Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay 49 9 3

Discovery of 20 novel ribosomal leaders in bacteria and archaea 49 31 8

Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates 136 49 8

Oxidized RNA Bodies compartmentalize translation quality control in Saccharomyces cerevisiae 49 34 3

An interaction network of RNA-binding proteins involved in Drosophila oogenesis 49 45 34 9 8 3

A systematic survey of PRMT interactomes reveals the key roles of arginine methylation in the global control of RNA splicing and translation 49 3

Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in protein translation 49 16 3

An alternative spliceosome defined by distinct snRNAs in early zebrafish embryogenesis 49 9

Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells 49 3

TRAP-based allelic translation efficiency imbalance analysis to identify genetic regulation of ribosome occupancy in specific cell types in vivo. 49 9

Direct measurements of mRNA translation kinetics in living cells 136 49 8

Translation-dependent and independent mRNA decay occur through mutually exclusive pathways that are defined by ribosome density during T Cell activation. 49 3

DDX3 depletion represses translation of mRNAs with complex 5' UTRs 49 3

Regulatory roles of 5' UTR and ORF-internal RNAs detected by 3' end mapping 49 31 9 3

Single-molecule imaging reveals translation of mRNAs localized to stress granules 49 34 3

ELAVL1 Primarily Couples mRNA Stability with the 3'UTRs of Interferon Stimulated Genes 49 27 3

The RNA helicase DHX30 coordinates cytoplasmic translation and mitochondrial function contributing to cancer cell survival 49 3

Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition interface 49 31 8 3

Networks of Splice Factor Regulation by Unproductive Splicing Coupled With Nonsense Mediated mRNA Decay 49 31 9 3

Sequence determinants and evolution of splicing in budding yeast and related species 49 9 3

The RNA-binding protein Puf5 buffers mRNA levels against chromatin-mediated changes in nascent transcription 49 31 3

Stage-Specific Long Non-coding RNAs in Cryptosporidium parvum as Revealed by Stranded RNA-Seq 49 9

RNA promotes the formation of spatial compartments in the nucleus 89 31 9 8 3

The transcription and export complex THO/TREX contributes to transcription termination in plants 49 16 3

METTL5, an 18S rRNA-specific m6A methyltransferase, modulates expression of stress response genes 49 3

Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation 49 31 9 3

Alteration of ribosome function upon 5-fluorouracil treatment favours cancer cell drug-tolerance 49 14 3

Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences 49 41 3

Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo 49 31 3

Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis 49 3

Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 NSP1 protein 49 41 31 3

LincRNA sequences are biased to counteract their translation 49 9

Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea 49 3

Limited but gene-class specific correlation of mRNA and protein expression in human CD8+ T cells 49 9 3

Deep conservation of ribosome stall sites across RNA processing genes 49 9

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition 49 20 3

Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1st and 2nd chemical steps 49 9 3

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing 49 31 9 3

Abundant circular RNA expression in terminal myeloid differentiation does not correlate with frequent circRNA translation, or with circRNA-mediated translation regulation 49 9 3

Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex 9

The Human Fragile X Mental Retardation Protein Inhibits the Elongation Step of Translation through its RGG and C-terminal domains 49 3

Post-transcriptional regulation of human endogenous retroviruses by RNA-Binding Motif Protein 4, RBM4 49 9 3

Molecular Functions of Conserved Developmentally-Regulated GTP-Binding Protein Drg1 in Translation 136 7 3

Inflammation Drives Alternative First Exon usage to Regulate Immune Genes including a Novel Iron Regulated Isoform of Aim2 7 3

CRISPR-TRAPSeq identifies the QKI RNA binding protein as important for astrocytic maturation and control of thalamocortical synapses. 49 3

RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines 49 9

Antisense ncRNAs during early vertebrate development are divided in groups with distinct features 134 49 9

GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation 134 49 9

Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage 134 9

A novel role for the C-terminal domain of the influenza A virus host shutoff endoribonuclease PA-X in mediating rapid turnover of the PA-X protein 41 3

The 3UTR of the orb2 gene encoding the Drosophila CPEB translation factor plays a critical role in spermatogenesis 49 20 3

Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast 49 31 9 3

Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identifies disease-relevant transcripts containing G-rich motifs. 49 9 3

Snord67 promotes lymph node metastasis and regulates U6-mediated alternative splicing in breast cancer 142 49 14 3

Alternative splicing coupled nonsense-mediated decay shapes the temperature-dependent transcriptome 49 3

Diversity and prevalence of ANTAR RNAs across actinobacteria 49 31 8 3

A Drosophila Model of Pontocerebellar Hypoplasia Reveals a Critical Role for the RNA Exosome in Neurons 137 65 49 9 3

ELAV proteins bind and stabilize C/EBP mRNA in the induction of long-term memory in Aplysia 49 3

ARF suppresses 5'-terminal oligopyrimidine mRNA translation 49 3

The spatial distributions of pre-mRNAs suggest post-transcriptional splicing of specific introns within endogenous genes 49 3

MeCP2 gates spatial learning-induced alternative splicing events in the mouse hippocampus 49 11 3

Comparative poly(A)+ RNA interactome capture of fission yeast RNA exosome mutants reveals insights into RNA biogenesis 7 3

Aberrant regulation of a poison exon caused by a non-coding variant in Scn1a-associated epileptic encephalopathy 137 65 49 9

Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons 49 33

Genetic removal of p70 S6K1 corrects coding sequence length-dependent alterations in mRNA translation in fragile X syndrome mice 49 3

Ribosome profiling reveals ribosome stalling on tryptophan codons upon oxidative stress in fission yeast 49 3

The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes 31 20 9 5

Defining a critical enhancer near Nanog using chromatin-focused approaches identifies RNA Pol II recruitment as required for expression 31 9

Noncanonical targeting contributes significantly to miRNA-mediated regulation. 7

Human Prefoldin Modulates Co-transcriptional Pre-mRNA Splicing 119 49 34 31 3

Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6 49 31 9 3

Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation 136 49 1

Ribosome stalling caused by the Argonaute-miRNA-SGS3 complex regulates production of secondary siRNA biogenesis in plants 49 16 3

Dynamics and functional roles of splicing factor autoregulation 49 31 3

Evolutionarily Conserved Transcription Factors Drive the Oxidative Stress Response in Drosophila 134 31 9 3

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts 120 9 3

Dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) display distinct, regional expression patterns that correlate with tRNA expression 134 49 16 9 5

5' UTR recruitment of eIF4GI or DAP5 drives cap-independent translation for a subset of human mRNAs 49 3

A single N6-methyladenosine site in lncRNA HOTAIR regulates its function in breast cancer cells 49 31 3

mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage 49 20 3

Inferring translational heterogeneity from ribosome profiling data 49 9

RTEL1 Influences the Abundance and Localization of TERRA RNA 49 34 3

Purine-responsive expression of the Leishmania donovani NT3 purine nucleobase transporter is mediated by a conserved RNA stem-loop 49 3

Transcriptional regulation of ACSL1 by CHREBP and NF-kappa B in macrophages during hyperglycemia and inflammation 150 110 49 3

Evolutionary Conservation and Essential Function of Human and Maize RNA Binding Motif Protein 48 (RBM48) in U12-Type Intron Splicing 49 20 3

S1-Domain RNA-Binding Protein (CvfD) Is a New Post-Transcriptional Regulator That Mediates Cold Sensitivity, Phosphate Transport, and Virulence in Streptococcus pneumoniae D39 49 3

LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival 49 9

Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts 49 21 5

Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs 119 49 31 3

AGO HITS-CLIP in Adipose Tissue Reveals miR-29 as a Post-Transcriptional Regulator of Leptin 74 39 9 3

KH domain containing RNA-binding proteins coordinate with microRNAs to regulate Caenorhabditis elegans development 74 49 9 3

Learning and Sleep Have Divergent Effects on Cytosolic and Membrane-Associated Ribosomal mRNA Profiles in Hippocampal Neurons 49 11 3

Aberrant regulation of RNA splicing in sunflower hybrids may underlie intrinsic incompatibilities 132 21 5

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome 134 9 4