A comprehensive map of insulator elements for the Drosophila genome

Nicolas Nègre, Christopher D. Brown, Parantu K. Shah, Pouya Kheradpour, Carolyn A. Morrison, Jorja G. Henikoff, Xin Feng, Kami Ahmad, Steven Russell, Robert A H White, Lincoln Stein, Steven Henikoff, Manolis Kellis, Kevin P. White

Research output: Contribution to journalArticlepeer-review

249 Scopus citations


Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulation. We studied by ChIP-chip the genome-wide binding sites of 6 insulator-associated proteins-dCTCF, CP190, BEAF-32, Su(Hw), Mod(mdg4), and GAF-to obtain the first comprehensive map of insulator elements in Drosophila embryos. We identify over 14,000 putative insulators, including all classically defined insulators. We find two major classes of insulators defined by dCTCF/CP190/BEAF-32 and Su(Hw), respectively. Distributional analyses of insulators revealed that particular sub-classes of insulator elements are excluded between cis-regulatory elements and their target promoters; divide differentially expressed, alternative, and divergent promoters; act as chromatin boundaries; are associated with chromosomal breakpoints among species; and are embedded within active chromatin domains. Together, these results provide a map demarcating the boundaries of gene regulatory units and a framework for understanding insulator function during the development and evolution of Drosophila.

Original languageEnglish (US)
Article numbere1000814
JournalPLoS genetics
Issue number1
StatePublished - Jan 2010

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research


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