Nature and function of insulator protein binding sites in the Drosophila genome

  1. Vincenzo Pirrotta2,10
  1. 1Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden;
  2. 2Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA;
  3. 3Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA;
  4. 4Group of Telomere Biology, Institute of Gene Biology, Moscow, 119334, Russia;
  5. 5Division of Genetics, Department of Medicine, Brigham and Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
  6. 6Institute of Molecular and Cellular Biology, Novosibirsk, 630090, Russia;
  7. 7Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
  8. 8Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
    1. 9 These authors contributed equally to this work.

    Abstract

    Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but only at a small number of Polycomb target regions and only to prevent repressive histone methylation within adjacent genes that are already transcriptionally inactive. RNAi knockdown of insulator proteins in cultured cells does not lead to major alterations in genome expression. Taken together, these observations argue against the concept of a genome partitioned by specialized boundary elements and suggest that insulators are reserved for specific regulation of selected genes.

    Footnotes

    • 10 Corresponding authors

      E-mail yuri.schwartz{at}molbiol.umu.se

      E-mail pirrotta{at}biology.rutgers.edu

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.138156.112.

    • Received January 26, 2012.
    • Accepted July 5, 2012.

    This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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