TY - JOUR
T1 - A comprehensive map of insulator elements for the Drosophila genome
AU - Nègre, Nicolas
AU - Brown, Christopher D.
AU - Shah, Parantu K.
AU - Kheradpour, Pouya
AU - Morrison, Carolyn A.
AU - Henikoff, Jorja G.
AU - Feng, Xin
AU - Ahmad, Kami
AU - Russell, Steven
AU - White, Robert A H
AU - Stein, Lincoln
AU - Henikoff, Steven
AU - Kellis, Manolis
AU - White, Kevin P.
PY - 2010/1
Y1 - 2010/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=76749089660&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=76749089660&partnerID=8YFLogxK
U2 - 10.1371/journal.pgen.1000814
DO - 10.1371/journal.pgen.1000814
M3 - Article
C2 - 20084099
AN - SCOPUS:76749089660
SN - 1553-7390
VL - 6
JO - PLoS genetics
JF - PLoS genetics
IS - 1
M1 - e1000814
ER -