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Comparative analysis of the transcriptome across distant species

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Listed:
  • Mark B. Gerstein

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, 51 Prospect Street, New Haven, Connecticut 06511, USA)

  • Joel Rozowsky

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Koon-Kiu Yan

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Daifeng Wang

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Chao Cheng

    (Geisel School of Medicine at Dartmouth
    Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth)

  • James B. Brown

    (Lawrence Berkeley National Laboratory
    University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA)

  • Carrie A. Davis

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • LaDeana Hillier

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

  • Cristina Sisu

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Jingyi Jessica Li

    (University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA
    University of California
    University of California)

  • Baikang Pei

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Arif O. Harmanci

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Michael O. Duff

    (Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA)

  • Sarah Djebali

    (Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
    Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain)

  • Roger P. Alexander

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Burak H. Alver

    (Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA)

  • Raymond Auerbach

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Kimberly Bell

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Peter J. Bickel

    (University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA)

  • Max E. Boeck

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

  • Nathan P. Boley

    (Lawrence Berkeley National Laboratory
    University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA)

  • Benjamin W. Booth

    (Lawrence Berkeley National Laboratory)

  • Lucy Cherbas

    (Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA
    Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA)

  • Peter Cherbas

    (Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA
    Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA)

  • Chao Di

    (MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University)

  • Alex Dobin

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Jorg Drenkow

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Brent Ewing

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

  • Gang Fang

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Megan Fastuca

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Elise A. Feingold

    (National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA)

  • Adam Frankish

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Guanjun Gao

    (MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University)

  • Peter J. Good

    (National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA)

  • Roderic Guigó

    (Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
    Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain)

  • Ann Hammonds

    (Lawrence Berkeley National Laboratory)

  • Jen Harrow

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Roger A. Hoskins

    (Lawrence Berkeley National Laboratory)

  • Cédric Howald

    (Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland
    Swiss Institute of Bioinformatics, Genopode building, Lausanne 1015, Switzerland)

  • Long Hu

    (MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University)

  • Haiyan Huang

    (University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA)

  • Tim J. P. Hubbard

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Medical and Molecular Genetics, King's College London, London WC2R 2LS, UK)

  • Chau Huynh

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

  • Sonali Jha

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Dionna Kasper

    (Yale University School of Medicine)

  • Masaomi Kato

    (Cellular and Developmental Biology, PO Box 208103, Yale University)

  • Thomas C. Kaufman

    (Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA)

  • Robert R. Kitchen

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Erik Ladewig

    (Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA)

  • Julien Lagarde

    (Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
    Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain)

  • Eric Lai

    (Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA)

  • Jing Leng

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Zhi Lu

    (MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University)

  • Michael MacCoss

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

  • Gemma May

    (Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA
    Carnegie Mellon University)

  • Rebecca McWhirter

    (Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA)

  • Gennifer Merrihew

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

  • David M. Miller

    (Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA)

  • Ali Mortazavi

    (Developmental and Cell Biology, University of California
    Center for Complex Biological Systems, University of California)

  • Rabi Murad

    (Developmental and Cell Biology, University of California
    Center for Complex Biological Systems, University of California)

  • Brian Oliver

    (Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health)

  • Sara Olson

    (Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA)

  • Peter J. Park

    (Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA)

  • Michael J. Pazin

    (National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA)

  • Norbert Perrimon

    (Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA)

  • Dmitri Pervouchine

    (Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
    Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain)

  • Valerie Reinke

    (Yale University School of Medicine)

  • Alexandre Reymond

    (Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland)

  • Garrett Robinson

    (University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA)

  • Anastasia Samsonova

    (Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA)

  • Gary I. Saunders

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK)

  • Felix Schlesinger

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Anurag Sethi

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Frank J. Slack

    (Cellular and Developmental Biology, PO Box 208103, Yale University)

  • William C. Spencer

    (Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA)

  • Marcus H. Stoiber

    (Lawrence Berkeley National Laboratory
    University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA)

  • Pnina Strasbourger

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

  • Andrea Tanzer

    (Bioinformatics and Genomics Programme, Center for Genomic Regulation, Universitat Pompeu Fabra (CRG-UPF), 08003 Barcelona, Catalonia, Spain
    Institute for Theoretical Chemistry, Theoretical Biochemistry Group (TBI), University of Vienna, Währingerstrasse 17/3/303, A-1090 Vienna, Austria)

  • Owen A. Thompson

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

  • Kenneth H. Wan

    (Lawrence Berkeley National Laboratory)

  • Guilin Wang

    (Yale University School of Medicine)

  • Huaien Wang

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Kathie L. Watkins

    (Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA)

  • Jiayu Wen

    (Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA)

  • Kejia Wen

    (MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University)

  • Chenghai Xue

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Li Yang

    (Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA
    Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Kevin Yip

    (Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
    5 CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong)

  • Chris Zaleski

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Yan Zhang

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Henry Zheng

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Steven E. Brenner

    (University of California
    University of California)

  • Brenton R. Graveley

    (Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA)

  • Susan E. Celniker

    (Lawrence Berkeley National Laboratory)

  • Thomas R. Gingeras

    (Functional Genomics, Cold Spring Harbor Laboratory)

  • Robert Waterston

    (William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA)

Abstract

Uniform processing and detailed annotation of human, worm and fly RNA-sequencing data reveal ancient, conserved features of the transcriptome, shared co-expression modules (many enriched in developmental genes), matched expression patterns across development and similar extent of non-canonical, non-coding transcription; furthermore, the data are used to create a single, universal model to predict gene-expression levels for all three organisms from chromatin features at the promoter.

Suggested Citation

  • Mark B. Gerstein & Joel Rozowsky & Koon-Kiu Yan & Daifeng Wang & Chao Cheng & James B. Brown & Carrie A. Davis & LaDeana Hillier & Cristina Sisu & Jingyi Jessica Li & Baikang Pei & Arif O. Harmanci & , 2014. "Comparative analysis of the transcriptome across distant species," Nature, Nature, vol. 512(7515), pages 445-448, August.
    • Handle: RePEc:nat:nature:v:512:y:2014:i:7515:d:10.1038_nature13424
    DOI: 10.1038/nature13424
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