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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

Author

Listed:
  • Peter V. Kharchenko

    (Center for Biomedical Informatics, Harvard Medical School
    Children’s Hospital Informatics Program)

  • Artyom A. Alekseyenko

    (Brigham & Women’s Hospital
    Harvard Medical School)

  • Yuri B. Schwartz

    (Rutgers University
    Present addresses: Department of Molecular Biology, Umea University, 901 87 Umea, Sweden. (Y.B.S.); Department of Plant Biology and Pathology, SEBS, Rutgers University, New Brunswick, New Jersey 08901, USA (D.L.-B.); Department of Basic Sciences, The Commonwealth Medical College, Scranton, Pennsylvania 18510, USA (G.S.).)

  • Aki Minoda

    (University of California at Berkeley, Lawrence Berkeley National Lab)

  • Nicole C. Riddle

    (Washington University in St Louis)

  • Jason Ernst

    (MIT Computer Science and Artificial Intelligence Laboratory
    Broad Institute of MIT and Harvard)

  • Peter J. Sabo

    (University of Washington)

  • Erica Larschan

    (Brigham & Women’s Hospital
    Harvard Medical School
    Cell Biology and Biochemistry, Brown University)

  • Andrey A. Gorchakov

    (Brigham & Women’s Hospital
    Harvard Medical School)

  • Tingting Gu

    (Washington University in St Louis)

  • Daniela Linder-Basso

    (Rutgers University
    Present addresses: Department of Molecular Biology, Umea University, 901 87 Umea, Sweden. (Y.B.S.); Department of Plant Biology and Pathology, SEBS, Rutgers University, New Brunswick, New Jersey 08901, USA (D.L.-B.); Department of Basic Sciences, The Commonwealth Medical College, Scranton, Pennsylvania 18510, USA (G.S.).)

  • Annette Plachetka

    (Brigham & Women’s Hospital
    Harvard Medical School)

  • Gregory Shanower

    (Rutgers University
    Present addresses: Department of Molecular Biology, Umea University, 901 87 Umea, Sweden. (Y.B.S.); Department of Plant Biology and Pathology, SEBS, Rutgers University, New Brunswick, New Jersey 08901, USA (D.L.-B.); Department of Basic Sciences, The Commonwealth Medical College, Scranton, Pennsylvania 18510, USA (G.S.).)

  • Michael Y. Tolstorukov

    (Center for Biomedical Informatics, Harvard Medical School
    Children’s Hospital Informatics Program)

  • Lovelace J. Luquette

    (Center for Biomedical Informatics, Harvard Medical School)

  • Ruibin Xi

    (Center for Biomedical Informatics, Harvard Medical School)

  • Youngsook L. Jung

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

  • Richard W. Park

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

  • Eric P. Bishop

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

  • Theresa K. Canfield

    (University of Washington)

  • Richard Sandstrom

    (University of Washington)

  • Robert E. Thurman

    (University of Washington)

  • David M. MacAlpine

    (Duke University Medical Center)

  • John A. Stamatoyannopoulos

    (University of Washington
    University of Washington)

  • Manolis Kellis

    (MIT Computer Science and Artificial Intelligence Laboratory
    Broad Institute of MIT and Harvard)

  • Sarah C. R. Elgin

    (Washington University in St Louis)

  • Mitzi I. Kuroda

    (Brigham & Women’s Hospital
    Harvard Medical School)

  • Vincenzo Pirrotta

    (Rutgers University)

  • Gary H. Karpen

    (University of California at Berkeley, Lawrence Berkeley National Lab)

  • Peter J. Park

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

Abstract

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.

Suggested Citation

  • Peter V. Kharchenko & Artyom A. Alekseyenko & Yuri B. Schwartz & Aki Minoda & Nicole C. Riddle & Jason Ernst & Peter J. Sabo & Erica Larschan & Andrey A. Gorchakov & Tingting Gu & Daniela Linder-Basso, 2011. "Comprehensive analysis of the chromatin landscape in Drosophila melanogaster," Nature, Nature, vol. 471(7339), pages 480-485, March.
    • Handle: RePEc:nat:nature:v:471:y:2011:i:7339:d:10.1038_nature09725
    DOI: 10.1038/nature09725
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    Cited by:

    1. Mujahid Ali & Lubna Younas & Jing Liu & Huangyi He & Xinpei Zhang & Qi Zhou, 2024. "Development and evolution of Drosophila chromatin landscape in a 3D genome context," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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