Comparative analysis of the transcriptome across distant species

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, Michael O. Duff, Sarah Djebali, Roger P. Alexander, Burak H. Alver, Raymond Auerbach, Kimberly Bell, Peter J. Bickel, Max E. Boeck, Nathan P. Boley, Benjamin W. Booth, Lucy Cherbas, Peter Cherbas, Chao Di, Alex Dobin, Jorg Drenkow, Brent Ewing, Gang Fang, Megan Fastuca, Elise A. Feingold, Adam Frankish, Guanjun Gao, Peter J. Good, Roderic Guigó, Ann Hammonds, Jen Harrow, Roger A. Hoskins, Cédric Howald, Long Hu, Haiyan Huang, Tim J. P. Hubbard, Chau Huynh, Sonali Jha, Dionna Kasper, Masaomi Kato, Thomas C. Kaufman, Robert R. Kitchen, Erik Ladewig, Julien Lagarde, Eric Lai, Jing Leng, Zhi Lu, Michael MacCoss, Gemma May, Rebecca McWhirter (), Gennifer Merrihew, David M. Miller, Ali Mortazavi, Rabi Murad, Brian Oliver, Sara Olson, Peter J. Park, Michael J. Pazin, Norbert Perrimon, Dmitri Pervouchine, Valerie Reinke, Alexandre Reymond, Garrett Robinson, Anastasia Samsonova, Gary I. Saunders, Felix Schlesinger, Anurag Sethi, Frank J. Slack, William C. Spencer, Marcus H. Stoiber, Pnina Strasbourger, Andrea Tanzer, Owen A. Thompson, Kenneth H. Wan, Guilin Wang, Huaien Wang, Kathie L. Watkins, Jiayu Wen, Kejia Wen, Chenghai Xue, Li Yang, Kevin Yip, Chris Zaleski, Yan Zhang, Henry Zheng, Steven E. Brenner (), Brenton R. Graveley (), Susan E. Celniker (), Thomas R. Gingeras () and Robert Waterston
Additional contact information
Mark B. Gerstein: Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
Joel Rozowsky: Program in Computational Biology and Bioinformatics, 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
Daifeng Wang: Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
Chao Cheng: Geisel School of Medicine at Dartmouth
James B. Brown: Lawrence Berkeley National Laboratory
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
Jingyi Jessica Li: University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA
Baikang Pei: Program in Computational Biology and Bioinformatics, 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
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
Roger P. Alexander: Program in Computational Biology and Bioinformatics, 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
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
Benjamin W. Booth: Lawrence Berkeley National Laboratory
Lucy Cherbas: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA
Peter Cherbas: 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
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
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
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
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
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
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
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
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
Rabi Murad: Developmental and Cell Biology, 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
Dmitri Pervouchine: Centre for Genomic Regulation, Doctor Aiguader 88, 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
Gary I. Saunders: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, 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
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
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
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
Kevin Yip: Hong Kong Bioinformatics Centre, 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
Henry Zheng: Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
Steven E. Brenner: 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

Nature, 2014, vol. 512, issue 7515, 445-448

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.

Date: 2014
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DOI: 10.1038/nature13424

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