A Comprehensive Map of Insulator Elements for the Drosophila Genome

Negre, N., Brown, C. D., Shah, P. K., Kheradpour, P., Morrison, C. A., Henikoff, J. G., Feng, X., Ahmad, K., Russell, S., White, R. A. H., Stein, L. D., Henikoff, S., Kellis, M., White, K. P. (January 2010) A Comprehensive Map of Insulator Elements for the Drosophila Genome. Plos Genetics, 6 (1). ISSN 1553-7390

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URL: https://www.ncbi.nlm.nih.gov/pubmed/20084099
DOI: 10.1371/journal.pgen.1000814

Abstract

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.

Item Type: Paper
Uncontrolled Keywords: ENHANCER-BLOCKING ACTIVITY EMBRYONIC STEM-CELLS FACTOR-BINDING SITES HAIRY-WING PROTEIN CHROMATIN INSULATOR BOUNDARY-ELEMENT CHROMOSOMAL DOMAINS SU(HW) INSULATOR GAGA-FACTOR CHIP-CHIP
Subjects: organism description > animal > insect > Drosophila
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Chromatin dynamics
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: CSHL Librarian
Date: January 2010
Date Deposited: 05 Oct 2011 14:49
Last Modified: 13 Mar 2018 13:27
PMCID: PMC2797089
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15496

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