Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation

[1]  Mei Wang,et al.  INTAC endonuclease and phosphatase modules differentially regulate transcription by RNA polymerase II. , 2023, Molecular cell.

[2]  Xuejun Jiang,et al.  H3K4me3 regulates RNA polymerase II promoter-proximal pause-release , 2023, Nature.

[3]  H. Siomi,et al.  Transcription of MERVL retrotransposons is required for preimplantation embryo development , 2023, Nature Genetics.

[4]  K. Adelman,et al.  U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes. , 2023, Molecular cell.

[5]  E. Wagner,et al.  Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci. , 2022, Molecular cell.

[6]  F. X. Chen,et al.  Coordinated regulation of RNA polymerase II pausing and elongation progression by PAF1 , 2022, Science advances.

[7]  A. Sandelin,et al.  Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression , 2022, Molecular cell.

[8]  Z. Izsvák,et al.  Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells. , 2022, Cell stem cell.

[9]  N. Proudfoot,et al.  Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics , 2022, Nature Reviews Molecular Cell Biology.

[10]  G. Pertea,et al.  Improved transcriptome assembly using a hybrid of long and short reads with StringTie , 2021, bioRxiv.

[11]  S. Bloor,et al.  Genome surveillance by HUSH-mediated silencing of intronless mobile elements , 2021, Nature.

[12]  M. Primig,et al.  EXOSC10/Rrp6 is essential for the eight-cell embryo/morula transition , 2021, bioRxiv.

[13]  T. Macfarlan,et al.  Transposable elements shape the evolution of mammalian development , 2021, Nature Reviews Genetics.

[14]  B. Cairns,et al.  p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models , 2021, Nature Genetics.

[15]  R. Andersson,et al.  Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells , 2021, bioRxiv.

[16]  Bo Peng,et al.  Mouse totipotent stem cells captured and maintained through spliceosomal repression , 2021, Cell.

[17]  S. Chanda,et al.  TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation , 2021, Cell.

[18]  A. Hutchins,et al.  Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE , 2021, Nature Communications.

[19]  Siyuan Lin,et al.  The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity , 2021, Nature.

[20]  Y. Shi,et al.  METTL3 regulates heterochromatin in mouse embryonic stem cells , 2021, Nature.

[21]  Aurélie Teissandier,et al.  m6A RNA methylation regulates the fate of endogenous retroviruses , 2021, Nature.

[22]  J. Rossant,et al.  Evaluating totipotency using criteria of increasing stringency , 2021, Nature Cell Biology.

[23]  R. Piro,et al.  SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency , 2020, BMC Bioinformatics.

[24]  L. Joosten,et al.  Trained Immunity-Promoting Nanobiologic Therapy Suppresses Tumor Growth and Potentiates Checkpoint Inhibition , 2020, Cell.

[25]  Ting Wang,et al.  Tissue-specific usage of transposable element-derived promoters in mouse development , 2020, Genome biology.

[26]  M. Torres-Padilla,et al.  The molecular and cellular features of 2-cell-like cells: a reference guide , 2020, Development.

[27]  S. Goff,et al.  Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview , 2020, Viruses.

[28]  P. Cramer,et al.  Integrator is a genome-wide attenuator of non-productive transcription , 2020, bioRxiv.

[29]  Xiaochen Bo,et al.  High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing , 2020, Nature Communications.

[30]  Xudong Fu,et al.  A transcriptional roadmap for 2C-like–to–pluripotent state transition , 2020, Science Advances.

[31]  Mark Wossidlo,et al.  Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage , 2020, Science Advances.

[32]  Jianlong Wang,et al.  DUX-miR-344-ZMYM2-Mediated Activation of MERVL LTRs Induces a Totipotent 2C-like State. , 2020, Cell stem cell.

[33]  S. Mirarab,et al.  Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.

[34]  A. Sandelin,et al.  A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome. , 2020, Cell reports.

[35]  Chuan He,et al.  N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription , 2020, Science.

[36]  Yangming Wang,et al.  SETDB1-Mediated Cell Fate Transition between 2C-Like and Pluripotent States. , 2020, Cell reports.

[37]  L. Maquat,et al.  Cellular RNA surveillance in health and disease , 2019, Science.

[38]  Ferhat Ay,et al.  Identification of significant chromatin contacts from HiChIP data by FitHiChIP , 2019, Nature Communications.

[39]  Yoshiaki Tanaka,et al.  The RNA exosome nuclease complex regulates human embryonic stem cell differentiation , 2019, The Journal of cell biology.

[40]  Xudong Fu,et al.  Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells , 2019, Nature Cell Biology.

[41]  Jennifer L Hu,et al.  MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices , 2019, Nature Methods.

[42]  Paul J. Hoffman,et al.  Comprehensive Integration of Single-Cell Data , 2018, Cell.

[43]  E. Furlong,et al.  Developmental enhancers and chromosome topology , 2018, Science.

[44]  Leighton J. Core,et al.  The RNA exosome contributes to gene expression regulation during stem cell differentiation , 2018, Nucleic acids research.

[45]  Xiaohua Shen,et al.  A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity , 2018, Cell.

[46]  T. Jensen,et al.  Controlling nuclear RNA levels , 2018, Nature Reviews Genetics.

[47]  James E. Bradner,et al.  The dTAG system for immediate and target-specific protein degradation , 2018, Nature Chemical Biology.

[48]  Andrea J. Kriz,et al.  Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP. , 2018, Molecular cell.

[49]  H. Madhani,et al.  Ten principles of heterochromatin formation and function , 2017, Nature Reviews Molecular Cell Biology.

[50]  Juan M. Vaquerizas,et al.  A molecular roadmap for the emergence of early-embryonic-like cells in culture , 2017, Nature Genetics.

[51]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[52]  Yi Xing,et al.  CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome , 2017, Nucleic acids research.

[53]  Wei Li,et al.  Correction: Human mutations in integrator complex subunits link transcriptome integrity to brain development , 2017, PLoS genetics.

[54]  J. V. Moran,et al.  Mobile DNA in Health and Disease , 2017, The New England journal of medicine.

[55]  C. Lima,et al.  Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase , 2017, eLife.

[56]  M. Surani,et al.  Activation of Lineage Regulators and Transposable Elements across a Pluripotent Spectrum , 2017, Stem cell reports.

[57]  B. Ren,et al.  KDM1A maintains genome-wide homeostasis of transcriptional enhancers , 2017, bioRxiv.

[58]  Robyn M. Kaake,et al.  The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity , 2017, Cell.

[59]  S. Tapscott,et al.  Conserved roles for murine DUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons , 2017, Nature Genetics.

[60]  R. Rabadán,et al.  Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry , 2017, Cell.

[61]  Russell B. Fletcher,et al.  Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics , 2017, BMC Genomics.

[62]  Kin Chung Lam,et al.  High-resolution TADs reveal DNA sequences underlying genome organization in flies , 2017, Nature Communications.

[63]  K. C. K. Lloyd,et al.  Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells , 2017, Science.

[64]  G. Schotta,et al.  Silencing of endogenous retroviruses by heterochromatin , 2017, Cellular and Molecular Life Sciences.

[65]  J. Wysocka,et al.  Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution , 2016, Cell.

[66]  R. Jaenisch,et al.  Molecular Criteria for Defining the Naive Human Pluripotent State , 2016, Cell stem cell.

[67]  Yan Li,et al.  SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation , 2016, PloS one.

[68]  Ricardo J. Miragaia,et al.  MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs , 2016, Cell reports.

[69]  Miao Yu,et al.  Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq , 2016, Cell Research.

[70]  Howard Y. Chang,et al.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.

[71]  M. Surani,et al.  Specification and epigenetic programming of the human germ line , 2016, Nature Reviews Genetics.

[72]  J. Gagneur,et al.  TT-seq maps the human transient transcriptome , 2016, Science.

[73]  Yaobo Xu,et al.  Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy , 2016, Human molecular genetics.

[74]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[75]  Gene W. Yeo,et al.  Robust transcriptome-wide discovery of RNA binding protein binding sites with enhanced CLIP (eCLIP) , 2016, Nature Methods.

[76]  M. Rosenfeld,et al.  Enhancers as non-coding RNA transcription units: recent insights and future perspectives , 2016, Nature Reviews Genetics.

[77]  J. Gagneur,et al.  Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN , 2016, bioRxiv.

[78]  Aurélie Teissandier,et al.  An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells , 2016, eLife.

[79]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[80]  M. Hammell,et al.  TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets , 2015, Bioinform..

[81]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[82]  B. Göttgens,et al.  Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells , 2015, Science.

[83]  Alexander J. Federation,et al.  RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity , 2015, Cell.

[84]  J. Simon,et al.  Gene Length Matters in Neurons , 2015, Neuron.

[85]  M. Pavlicev,et al.  Detecting Endogenous Retrovirus-Driven Tissue-Specific Gene Transcription , 2015, Genome biology and evolution.

[86]  Edwin Cuppen,et al.  Sambamba: fast processing of NGS alignment formats , 2015, Bioinform..

[87]  Yi Zhang,et al.  Cell totipotency: molecular features, induction, and maintenance. , 2015, National science review.

[88]  T. Jensen,et al.  The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis. , 2015, Cell reports.

[89]  Howard Y. Chang,et al.  ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide , 2015, Current protocols in molecular biology.

[90]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[91]  Leighton J. Core,et al.  Nuclear stability and transcriptional directionality separate functionally distinct RNA species , 2014, Nature Communications.

[92]  R. Rabadán,et al.  Noncoding RNA transcription targets AID to divergently transcribed loci in B cells , 2014, Nature.

[93]  Fidel Ramírez,et al.  deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..

[94]  A. Sandelin,et al.  Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance , 2014, Nature Genetics.

[95]  D. Guallar,et al.  Regulation of Mouse Retroelement MuERV-L/MERVL Expression by REX1 and Epigenetic Control of Stem Cell Potency , 2014, Front. Oncol..

[96]  T. Jensen,et al.  Dealing with pervasive transcription. , 2013, Molecular cell.

[97]  Stormy J. Chamberlain,et al.  Topoisomerases facilitate transcription of long genes linked to autism , 2013, Nature.

[98]  Steven J. M. Jones,et al.  Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells , 2013, Epigenetics & Chromatin.

[99]  T. Jensen,et al.  RNA decay machines: the exosome. , 2013, Biochimica et biophysica acta.

[100]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[101]  David A. Orlando,et al.  Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.

[102]  Helen M. Rowe,et al.  De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET , 2013, Development.

[103]  K. Hansen,et al.  BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions , 2012, Genome Biology.

[104]  Shawn P. Driscoll,et al.  ES cell potency fluctuates with endogenous retrovirus activity , 2012, Nature.

[105]  Jennifer Nichols,et al.  The Transcriptional and Epigenomic Foundations of Ground State Pluripotency , 2012, Cell.

[106]  D. Leung,et al.  Silencing of endogenous retroviruses: when and why do histone marks predominate? , 2012, Trends in biochemical sciences.

[107]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[108]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

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

[110]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[111]  Helen M. Rowe,et al.  KAP1 controls endogenous retroviruses in embryonic stem cells , 2010, Nature.

[112]  D. Tollervey,et al.  The Many Pathways of RNA Degradation , 2009, Cell.

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

[114]  Lokesh Kumar,et al.  Mfuzz: A software package for soft clustering of microarray data , 2007, Bioinformation.

[115]  J. Lis,et al.  The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila , 2002, Nature.

[116]  A. Nagy,et al.  Embryonic stem cells and mice expressing different GFP variants for multiple non-invasive reporter usage within a single animal , 2002, BMC biotechnology.

[117]  R. Beddington,et al.  An assessment of the developmental potential of embryonic stem cells in the midgestation mouse embryo. , 1989, Development.

[118]  Derrick J. Morton,et al.  The RNA Exosome and Human Disease. , 2020, Methods in molecular biology.

[119]  J. Gagneur,et al.  Molecular Systems Biology Peer Review Process File Annotation of Genomics Data Using Bidirectional Hidden Markov Models Unveils Variations in Pol Ii Transcription Cycle Transaction Report , 2022 .