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 journalArticle

202 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere1000814
JournalPLoS Genetics
Volume6
Issue number1
DOIs
StatePublished - Jan 2010

Fingerprint

Insulator Elements
Drosophila
Chromatin
chromatin
genome
Genome
promoter regions
regulatory sequences
gene
metazoan
Regulator Genes
regulator genes
embryo
binding sites
genomics
Embryonic Structures
Binding Sites
nucleotide sequences
DNA
protein

ASJC Scopus subject areas

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

Cite this

Nègre, N., Brown, C. D., Shah, P. K., Kheradpour, P., Morrison, C. A., Henikoff, J. G., ... White, K. P. (2010). A comprehensive map of insulator elements for the Drosophila genome. PLoS Genetics, 6(1), [e1000814]. https://doi.org/10.1371/journal.pgen.1000814

A comprehensive map of insulator elements for the Drosophila genome. / Nègre, Nicolas; Brown, Christopher D.; Shah, Parantu K.; Kheradpour, Pouya; Morrison, Carolyn A.; Henikoff, Jorja G.; Feng, Xin; Ahmad, Kami; Russell, Steven; White, Robert A H; Stein, Lincoln; Henikoff, Steven; Kellis, Manolis; White, Kevin P.

In: PLoS Genetics, Vol. 6, No. 1, e1000814, 01.2010.

Research output: Contribution to journalArticle

Nègre, N, Brown, CD, Shah, PK, Kheradpour, P, Morrison, CA, Henikoff, JG, Feng, X, Ahmad, K, Russell, S, White, RAH, Stein, L, Henikoff, S, Kellis, M & White, KP 2010, 'A comprehensive map of insulator elements for the Drosophila genome', PLoS Genetics, vol. 6, no. 1, e1000814. https://doi.org/10.1371/journal.pgen.1000814
Nègre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, Henikoff JG et al. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genetics. 2010 Jan;6(1). e1000814. https://doi.org/10.1371/journal.pgen.1000814
Nègre, Nicolas ; Brown, Christopher D. ; Shah, Parantu K. ; Kheradpour, Pouya ; Morrison, Carolyn A. ; Henikoff, Jorja G. ; Feng, Xin ; Ahmad, Kami ; Russell, Steven ; White, Robert A H ; Stein, Lincoln ; Henikoff, Steven ; Kellis, Manolis ; White, Kevin P. / A comprehensive map of insulator elements for the Drosophila genome. In: PLoS Genetics. 2010 ; Vol. 6, No. 1.
@article{4f4e9bc5f2634fad81c373b5bd77c510,
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.",
author = "Nicolas N{\`e}gre and Brown, {Christopher D.} and Shah, {Parantu K.} and Pouya Kheradpour and Morrison, {Carolyn A.} and Henikoff, {Jorja G.} and Xin Feng and Kami Ahmad and Steven Russell and White, {Robert A H} and Lincoln Stein and Steven Henikoff and Manolis Kellis and White, {Kevin P.}",
year = "2010",
month = "1",
doi = "10.1371/journal.pgen.1000814",
language = "English (US)",
volume = "6",
journal = "PLoS Genetics",
issn = "1553-7390",
publisher = "Public Library of Science",
number = "1",

}

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

VL - 6

JO - PLoS Genetics

JF - PLoS Genetics

SN - 1553-7390

IS - 1

M1 - e1000814

ER -