title: Histone modifications at human enhancers reflect global cell-type-specific gene expression.
abstract: The human body is composed of diverse cell types with distinct functions. Although it is known that lineage specification depends on cell-specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene, the relative roles of these regulatory elements in this process are not clear. We have previously developed a chromatin-immunoprecipitation-based microarray method (ChIP-chip) to locate promoters, enhancers and insulators in the human genome. Here we use the same approach to identify these elements in multiple cell types and investigate their roles in cell-type-specific gene expression. We observed that the chromatin state at promoters and CTCF-binding at insulators is largely invariant across diverse cell types. In contrast, enhancers are marked with highly cell-type-specific histone modification patterns, strongly correlate to cell-type-specific gene expression programs on a global scale, and are functionally active in a cell-type-specific manner. Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression.
authors.affiliation: Ludwig Institute for Cancer Research, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA.
authors.forename: Nathaniel D
authors.initials: ND
authors.lastname: Heintzman
authors.forename: Gary C
authors.initials: GC
authors.lastname: Hon
authors.forename: R David
authors.initials: RD
authors.lastname: Hawkins
authors.forename: Pouya
authors.initials: P
authors.lastname: Kheradpour
authors.forename: Alexander
authors.initials: A
authors.lastname: Stark
authors.forename: Lindsey F
authors.initials: LF
authors.lastname: Harp
authors.forename: Zhen
authors.initials: Z
authors.lastname: Ye
authors.forename: Leonard K
authors.initials: LK
authors.lastname: Lee
authors.forename: Rhona K
authors.initials: RK
authors.lastname: Stuart
authors.forename: Christina W
authors.initials: CW
authors.lastname: Ching
authors.forename: Keith A
authors.initials: KA
authors.lastname: Ching
authors.forename: Jessica E
authors.initials: JE
authors.lastname: Antosiewicz-Bourget
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.forename: Xinmin
authors.initials: X
authors.lastname: Zhang
authors.forename: Roland D
authors.initials: RD
authors.lastname: Green
authors.forename: Victor V
authors.initials: VV
authors.lastname: Lobanenkov
authors.forename: Ron
authors.initials: R
authors.lastname: Stewart
authors.forename: James A
authors.initials: JA
authors.lastname: Thomson
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Crawford
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Bing
authors.initials: B
authors.lastname: Ren
mesh_terms: D001665:Binding Sites; D002460:Cell Line; D002468:Cell Physiological Phenomena; D002843:Chromatin / Q000235:genetics; D005786:Gene Expression Regulation; D015894:Genome, Human / Q000235:genetics; D006367:HeLa Cells; D006657:Histones / Q000378:metabolism*; D006801:Humans; D020014:K562 Cells; D011401:Promoter Regions, Genetic / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D014157:Transcription Factors