5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader

[1]  D. Page,et al.  Two closely related human nuclear export factors utilize entirely distinct export pathways. , 2001, Molecular cell.

[2]  Jin Billy Li,et al.  Accurate identification of human Alu and non-Alu RNA editing sites , 2012, Nature Methods.

[3]  R. North,et al.  Calcium dependent regulation of Rab activation and vesicle fusion by an intracellular P2X ion channel , 2013, Nature Cell Biology.

[4]  O. Elemento,et al.  Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons , 2012, Cell.

[5]  Chuan He,et al.  Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. , 2016, Trends in genetics : TIG.

[6]  R. Gregory,et al.  The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells. , 2016, Molecular cell.

[7]  Yuanjiang Pan,et al.  Kinetic and Thermodynamic Control of Protonation in Atmospheric Pressure Chemical Ionization , 2013, Journal of The American Society for Mass Spectrometry.

[8]  Chuan He,et al.  FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis , 2014, Cell Research.

[9]  D. Meinel,et al.  Prp19C and TREX: Interacting to promote transcription elongation 
and mRNA export , 2012, Transcription.

[10]  Schraga Schwartz,et al.  Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs , 2013, PLoS genetics.

[11]  Jernej Ule,et al.  NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs , 2013, Cell reports.

[12]  F. Stutz,et al.  Keeping mRNPs in check during assembly and nuclear export , 2011, Nature Reviews Molecular Cell Biology.

[13]  Chengqi Yi,et al.  N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO , 2011, Nature chemical biology.

[14]  Saeed Tavazoie,et al.  HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events , 2015, Cell.

[15]  R. Reed,et al.  Coupling transcription, splicing and mRNA export. , 2003, Current opinion in cell biology.

[16]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[17]  J. Steitz,et al.  Protein Ligands to Hur Modulate Its Interaction with Target Mrnas in Vivo , 2000, The Journal of cell biology.

[18]  Bing Ren,et al.  N6-methyladenosine-dependent regulation of messenger RNA stability , 2013 .

[19]  Shiqing Ma,et al.  Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. , 2015, Nature chemical biology.

[20]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[21]  Vihandha O. Wickramasinghe,et al.  Control of mammalian gene expression by selective mRNA export , 2015, Nature Reviews Molecular Cell Biology.

[22]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[23]  W. Gilbert,et al.  Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells , 2014, Nature.

[24]  A. Bird,et al.  Purification, sequence, and cellular localization of a novel chromosomal protein that binds to Methylated DNA , 1992, Cell.

[25]  V. Wickramasinghe,et al.  mRNA Export from Mammalian Cell Nuclei Is Dependent on GANP , 2010, Current Biology.

[26]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[27]  Jun Li,et al.  Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs , 2017, Plant Cell.

[28]  R. Micura,et al.  Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain , 2017, Genome Biology.

[29]  SH Song,et al.  The BIG Data Center: from deposition to integration to translation , 2016, Nucleic Acids Res..

[30]  M. Kupiec,et al.  Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq , 2012, Nature.

[31]  Qian Zhang,et al.  GSA: Genome Sequence Archive* , 2017, Genom. Proteom. Bioinform..

[32]  K. Redman,et al.  RNA methyltransferases utilize two cysteine residues in the formation of 5-methylcytosine. , 2002, Biochemistry.

[33]  S. Tavazoie,et al.  N6-methyladenosine marks primary microRNAs for processing , 2015, Nature.

[34]  Maxwell R. Mumbach,et al.  Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA , 2014, Cell.

[35]  Olivier Elemento,et al.  5 0 UTR m 6 A Promotes Cap-Independent Translation Graphical , 2022 .

[36]  J. Katahira mRNA export and the TREX complex. , 2012, Biochimica et biophysica acta.

[37]  Brad T. Sherman,et al.  DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.

[38]  Chuan He,et al.  N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions , 2015, Nature.

[39]  Gideon Rechavi,et al.  The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA , 2016, Nature.

[40]  Jérôme Hugues,et al.  Model‐Based Analysis , 2013 .

[41]  Shankar Balasubramanian,et al.  Formation and Abundance of 5-Hydroxymethylcytosine in RNA , 2015, Chembiochem : a European journal of chemical biology.

[42]  Mark Helm,et al.  Post-transcriptional nucleotide modification and alternative folding of RNA , 2006, Nucleic acids research.

[43]  Frank Lyko,et al.  RNA cytosine methylation analysis by bisulfite sequencing , 2008, Nucleic acids research.

[44]  T. Preiss,et al.  Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA , 2012, Nucleic acids research.

[45]  E. Hurt,et al.  The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans , 2000, Nature.

[46]  Ed Hurt,et al.  Linking gene regulation to mRNA production and export. , 2011, Current opinion in cell biology.

[47]  Felix Krueger,et al.  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..

[48]  Chengqi Yi,et al.  Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. , 2016, Nature chemical biology.

[49]  R. Camerini-Otero,et al.  The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation , 2004, Nature Genetics.

[50]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[51]  S. Masuda,et al.  RNA Export through the NPC in Eukaryotes , 2015, Genes.

[52]  M. Frye,et al.  Posttranscriptional methylation of transfer and ribosomal RNA in stress response pathways, cell differentiation, and cancer , 2016, Current opinion in oncology.

[53]  Zhike Lu,et al.  m6A-dependent regulation of messenger RNA stability , 2013, Nature.

[54]  Ke Liu,et al.  Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. , 2014, Nature chemical biology.

[55]  R. Roeder,et al.  Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. , 1983, Nucleic acids research.

[56]  Ed Hurt,et al.  Exporting RNA from the nucleus to the cytoplasm , 2007, Nature Reviews Molecular Cell Biology.

[57]  C. Langford,et al.  Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP , 2014, Nucleic acids research.

[58]  W. Hong,et al.  A role for sorting nexin 27 in AMPA receptor trafficking , 2014, Nature Communications.

[59]  F. Tuorto,et al.  RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis , 2012, Nature Structural &Molecular Biology.

[60]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[61]  P. Thibault,et al.  Molecular dissection of the eukaryotic initiation factor 4E (eIF4E) export‐competent RNP , 2009, The EMBO journal.

[62]  M. Schaefer,et al.  RNA 5-Methylcytosine Analysis by Bisulfite Sequencing. , 2015, Methods in enzymology.

[63]  Samir Adhikari,et al.  Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. , 2016, Molecular cell.

[64]  Chuan He,et al.  N 6 -methyladenosine Modulates Messenger RNA Translation Efficiency , 2015, Cell.

[65]  Zhike Lu,et al.  Unique Features of the m6A Methylome in Arabidopsis thaliana , 2014, Nature Communications.

[66]  Yun-Gui Yang,et al.  Dynamic m6A modification and its emerging regulatory role in mRNA splicing , 2015 .

[67]  Alexander F. Palazzo,et al.  Sumoylation is Required for the Cytoplasmic Accumulation of a Subset of mRNAs , 2014, Genes.

[68]  Bradley R. Cairns,et al.  Identification of direct targets and modified bases of RNA cytosine methyltransferases , 2013, Nature Biotechnology.

[69]  Izabela Makałowska,et al.  Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA(CAA)Leu , 2006, Nucleic acids research.

[70]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[71]  Shu-Bing Qian,et al.  Dynamic m6A mRNA methylation directs translational control of heat shock response , 2015, Nature.

[72]  F. Waharte,et al.  The human TREX-2 complex is stably associated with the nuclear pore basket , 2013, Journal of Cell Science.

[73]  Chuan He,et al.  Post-transcriptional gene regulation by mRNA modifications , 2016, Nature Reviews Molecular Cell Biology.

[74]  Paul F Agris,et al.  Bringing order to translation: the contributions of transfer RNA anticodon‐domain modifications , 2008, EMBO reports.