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Comparative analysis of metazoan chromatin organization

Author

Listed:
  • Joshua W. K. Ho

    (Center for Biomedical Informatics, Harvard Medical School
    Brigham and Women’s Hospital, Harvard Medical School
    Present addresses: Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).)

  • Youngsook L. Jung

    (Center for Biomedical Informatics, Harvard Medical School
    Brigham and Women’s Hospital, Harvard Medical School)

  • Tao Liu

    (Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute
    Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
    Present addresses: Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).)

  • Burak H. Alver

    (Center for Biomedical Informatics, Harvard Medical School)

  • Soohyun Lee

    (Center for Biomedical Informatics, Harvard Medical School)

  • Kohta Ikegami

    (University of North Carolina at Chapel Hill
    Present addresses: Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).)

  • Kyung-Ah Sohn

    (Ajou University, Suwon 443-749, Korea
    Systems Biomedical Informatics Research Center, College of Medicine, Seoul National University, Seoul 110-799, Korea)

  • Aki Minoda

    (Lawrence Berkeley National Lab, Berkeley, California 94720, USA
    University of California, Berkeley, Berkeley, California 94720, USA
    Present addresses: Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).)

  • Michael Y. Tolstorukov

    (Center for Biomedical Informatics, Harvard Medical School
    Brigham and Women’s Hospital, Harvard Medical School
    Massachusetts General Hospital and Harvard Medical School)

  • Alex Appert

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Stephen C. J. Parker

    (National Institute of General Medical Sciences, National Institutes of Health
    National Human Genome Research Institute, National Institutes of Health)

  • Tingting Gu

    (Washington University in St. Louis)

  • Anshul Kundaje

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology
    Broad Institute
    Present addresses: Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).)

  • Nicole C. Riddle

    (Washington University in St. Louis
    Present addresses: Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).)

  • Eric Bishop

    (Center for Biomedical Informatics, Harvard Medical School
    Program in Bioinformatics, Boston University)

  • Thea A. Egelhofer

    (Cell and Developmental Biology, University of California Santa Cruz)

  • Sheng'en Shawn Hu

    (School of Life Science and Technology, Tongji University)

  • Artyom A. Alekseyenko

    (Brigham and Women’s Hospital, Harvard Medical School
    Harvard Medical School)

  • Andreas Rechtsteiner

    (Cell and Developmental Biology, University of California Santa Cruz)

  • Dalal Asker

    (Rutgers University
    Faculty of Agriculture, Alexandria University, 21545 El-Shatby, Alexandria, Egypt)

  • Jason A. Belsky

    (Duke University Medical Center)

  • Sarah K. Bowman

    (Massachusetts General Hospital and Harvard Medical School)

  • Q. Brent Chen

    (University of North Carolina at Chapel Hill)

  • Ron A.-J. Chen

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Daniel S. Day

    (Center for Biomedical Informatics, Harvard Medical School
    Harvard/MIT Division of Health Sciences and Technology)

  • Yan Dong

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Andrea C. Dose

    (University of California Davis)

  • Xikun Duan

    (School of Life Science and Technology, Tongji University)

  • Charles B. Epstein

    (Broad Institute)

  • Sevinc Ercan

    (University of North Carolina at Chapel Hill
    Center for Genomics and Systems Biology, New York University)

  • Elise A. Feingold

    (National Human Genome Research Institute, National Institutes of Health)

  • Francesco Ferrari

    (Center for Biomedical Informatics, Harvard Medical School)

  • Jacob M. Garrigues

    (Cell and Developmental Biology, University of California Santa Cruz)

  • Nils Gehlenborg

    (Center for Biomedical Informatics, Harvard Medical School
    Broad Institute)

  • Peter J. Good

    (National Human Genome Research Institute, National Institutes of Health)

  • Psalm Haseley

    (Center for Biomedical Informatics, Harvard Medical School
    Brigham and Women’s Hospital, Harvard Medical School)

  • Daniel He

    (University of California, Berkeley, Berkeley, California 94720, USA)

  • Moritz Herrmann

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Michael M. Hoffman

    (Princess Margaret Cancer Centre, Toronto, Ontario M6G 1L7, Canada)

  • Tess E. Jeffers

    (University of North Carolina at Chapel Hill
    Present addresses: Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).)

  • Peter V. Kharchenko

    (Center for Biomedical Informatics, Harvard Medical School)

  • Paulina Kolasinska-Zwierz

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Chitra V. Kotwaliwale

    (University of California, Berkeley, Berkeley, California 94720, USA
    Howard Hughes Medical Institute)

  • Nischay Kumar

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology
    Broad Institute)

  • Sasha A. Langley

    (Lawrence Berkeley National Lab, Berkeley, California 94720, USA
    University of California, Berkeley, Berkeley, California 94720, USA)

  • Erica N. Larschan

    (Cellular Biology and Biochemistry, Brown University)

  • Isabel Latorre

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Maxwell W. Libbrecht

    (University of Washington)

  • Xueqiu Lin

    (School of Life Science and Technology, Tongji University)

  • Richard Park

    (Center for Biomedical Informatics, Harvard Medical School
    Program in Bioinformatics, Boston University)

  • Michael J. Pazin

    (National Human Genome Research Institute, National Institutes of Health)

  • Hoang N. Pham

    (Lawrence Berkeley National Lab, Berkeley, California 94720, USA
    University of California, Berkeley, Berkeley, California 94720, USA
    Howard Hughes Medical Institute)

  • Annette Plachetka

    (Brigham and Women’s Hospital, Harvard Medical School
    Harvard Medical School)

  • Bo Qin

    (School of Life Science and Technology, Tongji University)

  • Yuri B. Schwartz

    (Rutgers University
    Umea University, 901 87 Umea, Sweden)

  • Noam Shoresh

    (Broad Institute)

  • Przemyslaw Stempor

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Anne Vielle

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Chengyang Wang

    (School of Life Science and Technology, Tongji University)

  • Christina M. Whittle

    (University of California, Berkeley, Berkeley, California 94720, USA
    Howard Hughes Medical Institute)

  • Huiling Xue

    (Center for Biomedical Informatics, Harvard Medical School
    Brigham and Women’s Hospital, Harvard Medical School)

  • Robert E. Kingston

    (Massachusetts General Hospital and Harvard Medical School)

  • Ju Han Kim

    (Systems Biomedical Informatics Research Center, College of Medicine, Seoul National University, Seoul 110-799, Korea
    Seoul National University Biomedical Informatics, College of Medicine, Seoul National University, Seoul 110-799, Korea)

  • Bradley E. Bernstein

    (Broad Institute
    Howard Hughes Medical Institute
    Massachusetts General Hospital and Harvard Medical School)

  • Abby F. Dernburg

    (Lawrence Berkeley National Lab, Berkeley, California 94720, USA
    University of California, Berkeley, Berkeley, California 94720, USA
    Howard Hughes Medical Institute)

  • Vincenzo Pirrotta

    (Rutgers University)

  • Mitzi I. Kuroda

    (Brigham and Women’s Hospital, Harvard Medical School
    Harvard Medical School)

  • William S. Noble

    (University of Washington
    University of Washington)

  • Thomas D. Tullius

    (Program in Bioinformatics, Boston University
    Boston University)

  • Manolis Kellis

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology
    Broad Institute)

  • David M. MacAlpine

    (Duke University Medical Center)

  • Susan Strome

    (Cell and Developmental Biology, University of California Santa Cruz)

  • Sarah C. R. Elgin

    (Washington University in St. Louis)

  • Xiaole Shirley Liu

    (Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute
    Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
    Broad Institute)

  • Jason D. Lieb

    (University of North Carolina at Chapel Hill
    Present addresses: Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).)

  • Julie Ahringer

    (University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK)

  • Gary H. Karpen

    (Lawrence Berkeley National Lab, Berkeley, California 94720, USA
    University of California, Berkeley, Berkeley, California 94720, USA)

  • Peter J. Park

    (Center for Biomedical Informatics, Harvard Medical School
    Brigham and Women’s Hospital, Harvard Medical School
    Informatics Program, Children's Hospital)

Abstract

A large collection of new modENCODE and ENCODE genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human are analysed; this reveals many conserved features of chromatin organization among the three organisms, as well as notable differences in the composition and locations of repressive chromatin.

Suggested Citation

  • Joshua W. K. Ho & Youngsook L. Jung & Tao Liu & Burak H. Alver & Soohyun Lee & Kohta Ikegami & Kyung-Ah Sohn & Aki Minoda & Michael Y. Tolstorukov & Alex Appert & Stephen C. J. Parker & Tingting Gu & , 2014. "Comparative analysis of metazoan chromatin organization," Nature, Nature, vol. 512(7515), pages 449-452, August.
    • Handle: RePEc:nat:nature:v:512:y:2014:i:7515:d:10.1038_nature13415
    DOI: 10.1038/nature13415
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