title: A comprehensive map of insulator elements for the Drosophila genome.
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.
authors.affiliation: Institute for Genomics and Systems Biology, Department of Human Genetics, and Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Nègre
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Brown
authors.forename: Parantu K
authors.initials: PK
authors.lastname: Shah
authors.forename: Pouya
authors.initials: P
authors.lastname: Kheradpour
authors.forename: Carolyn A
authors.initials: CA
authors.lastname: Morrison
authors.forename: Jorja G
authors.initials: JG
authors.lastname: Henikoff
authors.forename: Xin
authors.initials: X
authors.lastname: Feng
authors.forename: Kami
authors.initials: K
authors.lastname: Ahmad
authors.forename: Steven
authors.initials: S
authors.lastname: Russell
authors.forename: Robert A H
authors.initials: RA
authors.lastname: White
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
authors.forename: Steven
authors.initials: S
authors.lastname: Henikoff
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Kevin P
authors.initials: KP
authors.lastname: White
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004330:Drosophila / Q000235:genetics* / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D049750:Genome, Insect; D038101:Insulator Elements; D011485:Protein Binding
chemical_list: D029721:Drosophila Proteins