Comprehensive analysis of the chromatin landscape in Drosophila melanogaster View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-12-22

AUTHORS

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, Annette Plachetka, Gregory Shanower, Michael Y. Tolstorukov, Lovelace J. Luquette, Ruibin Xi, Youngsook L. Jung, Richard W. Park, Eric P. Bishop, Theresa K. Canfield, Richard Sandstrom, Robert E. Thurman, David M. MacAlpine, John A. Stamatoyannopoulos, Manolis Kellis, Sarah C. R. Elgin, Mitzi I. Kuroda, Vincenzo Pirrotta, Gary H. Karpen, Peter J. Park

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. More... »

PAGES

480-485

References to SciGraph publications

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  • Journal

    TITLE

    Nature

    ISSUE

    7339

    VOLUME

    471

    Author Affiliations

  • Children’s Hospital Informatics Program, 02115, Boston, Massachusetts, USA
  • Department of Genetics, Harvard Medical School, 02115, Boston, Massachusetts, USA
  • 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.).
  • Department of Molecular and Cell Biology, and Department of Genome Dynamics, University of California at Berkeley, Lawrence Berkeley National Lab, 94720, Berkeley, California, USA
  • Department of Biology, Washington University in St Louis, 63130, St Louis, Missouri, USA
  • Broad Institute of MIT and Harvard, 02142, Cambridge, Massachusetts, USA
  • Department of Genome Sciences, University of Washington, 98195, Seattle, Washington, USA
  • Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 02906, Providence, Rhode Island, USA
  • Center for Biomedical Informatics, Harvard Medical School, 02115, Boston, Massachusetts, USA
  • Division of Genetics, Department of Medicine, Brigham & Women’s Hospital, 02115, Boston, Massachusetts, USA
  • Graduate Program in Bioinformatics, Boston University, 02115, Boston, Massachusetts, USA
  • Department of Pharmacology and Cancer Biology, Duke University Medical Center, 27710, Durham, North Carolina, USA
  • Department of Medicine, University of Washington, 98195, Seattle, Washington, USA
  • Department of Molecular Biology and Biochemistry, Rutgers University, 08854, Piscataway, New Jersey, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature09725

    DOI

    http://dx.doi.org/10.1038/nature09725

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1023233286

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21179089


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