High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

[1]  Ashley R Bonneau,et al.  Zygotic genome activation during the maternal-to-zygotic transition. , 2014, Annual review of cell and developmental biology.

[2]  Ido Amit,et al.  4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells , 2014, Genome Biology.

[3]  Yong Zhang,et al.  Canonical nucleosome organization at promoters forms during genome activation , 2014, Genome research.

[4]  D. Bartel,et al.  Poly(A)-tail profiling reveals an embryonic switch in translational control , 2014, Nature.

[5]  Achim Tresch,et al.  Periodic mRNA synthesis and degradation co‐operate during cell cycle gene expression , 2014, Molecular systems biology.

[6]  I. Dawid Faculty Opinions recommendation of Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. , 2013 .

[7]  Miler T. Lee,et al.  Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition , 2013, Nature.

[8]  Daniel R. Caffrey,et al.  A Long Noncoding RNA Mediates Both Activation and Repression of Immune Response Genes , 2013, Science.

[9]  J. Stender,et al.  Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. , 2013, Molecular cell.

[10]  J. Rinn,et al.  Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs , 2013, Development.

[11]  D. Black,et al.  Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. , 2013, RNA.

[12]  P. Blackshear,et al.  Tristetraprolin (TTP): interactions with mRNA and proteins, and current thoughts on mechanisms of action. , 2013, Biochimica et biophysica acta.

[13]  Aviv Regev,et al.  Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples , 2013, Nature Methods.

[14]  Aviv Regev,et al.  Corrigendum: Comparative analysis of RNA sequencing methods for degraded or low-input samples , 2013, Nature Methods.

[15]  Nir Friedman,et al.  A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.

[16]  S. Kaufmann,et al.  Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution , 2012, Genome research.

[17]  Richard Durbin,et al.  High levels of RNA-editing site conservation amongst 15 laboratory mouse strains , 2012, Genome Biology.

[18]  Jacek Majewski,et al.  Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome” , 2012, Science.

[19]  Jin Billy Li,et al.  Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome” , 2012, Science.

[20]  Michael F. Lin,et al.  Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. , 2012, Genome research.

[21]  Cole Trapnell,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[22]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[23]  Mingyao Li,et al.  Widespread RNA and DNA Sequence Differences in the Human Transcriptome , 2011, Science.

[24]  N. Friedman,et al.  Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells , 2011, Nature Biotechnology.

[25]  J. Weissman,et al.  Nascent transcript sequencing visualizes transcription at nucleotide resolution , 2011, Nature.

[26]  Eytan Domany,et al.  Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli , 2013 .

[27]  E. Wang,et al.  Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.

[28]  N. Friedman,et al.  Comprehensive comparative analysis of strand-specific RNA sequencing methods , 2010, Nature Methods.

[29]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[30]  Scott B. Dewell,et al.  Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.

[31]  David Haussler,et al.  The UCSC Genome Browser database: update 2010 , 2009, Nucleic Acids Res..

[32]  Zachary D. Smith,et al.  Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses , 2009 .

[33]  R. Padgett,et al.  Rates of in situ transcription and splicing in large human genes , 2009, Nature Structural &Molecular Biology.

[34]  G. Church,et al.  Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing , 2009, Science.

[35]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[36]  Gal Chechik,et al.  Timing of Gene Expression Responses to Environmental Changes , 2009, J. Comput. Biol..

[37]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[38]  D. Koller,et al.  Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network , 2008, Nature Biotechnology.

[39]  Eran Segal,et al.  Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation , 2008, Molecular systems biology.

[40]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[41]  R. Zimmer,et al.  High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. , 2008, RNA.

[42]  Alexander F Schier,et al.  The Maternal-Zygotic Transition: Death and Birth of RNAs , 2007, Science.

[43]  David Haussler,et al.  The UCSC genome browser database: update 2007 , 2006, Nucleic Acids Res..

[44]  Joel S. Parker,et al.  Novel mRNA Targets for Tristetraprolin (TTP) Identified by Global Analysis of Stabilized Transcripts in TTP-Deficient Fibroblasts , 2006, Molecular and Cellular Biology.

[45]  Eli Eisenberg,et al.  RNA editing level in the mouse is determined by the genomic repeat repertoire. , 2006, RNA.

[46]  D. Barlow,et al.  The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export , 2006, The EMBO journal.

[47]  Anton J. Enright,et al.  Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs , 2006, Science.

[48]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[49]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[50]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[51]  D. Weil,et al.  In Vivo Kinetics of mRNA Splicing and Transport in Mammalian Cells , 2002, Molecular and Cellular Biology.

[52]  P. Blackshear,et al.  Feedback Inhibition of Macrophage Tumor Necrosis Factor-α Production by Tristetraprolin , 1998 .

[53]  P. Blackshear,et al.  Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin. , 1998, Science.

[54]  B. Haynes,et al.  A pathogenetic role for TNF alpha in the syndrome of cachexia, arthritis, and autoimmunity resulting from tristetraprolin (TTP) deficiency. , 1996, Immunity.

[55]  C. Kimmel,et al.  Stages of embryonic development of the zebrafish , 1995, Developmental dynamics : an official publication of the American Association of Anatomists.

[56]  AC Tose Cell , 1993, Cell.