Histone modifications at human enhancers reflect global cell-type-specific gene expression.

TitleHistone modifications at human enhancers reflect global cell-type-specific gene expression.
Publication TypeJournal Article
Year of Publication2009
AuthorsHeintzman ND, Hon GC, Hawkins DR, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B
JournalNature
Volume459
Issue7243
Pagination108-12
Date Published2009 May 7
ISSN1476-4687
KeywordsBinding Sites, Cell Line, Cell Physiological Phenomena, Chromatin, Gene Expression Regulation, Genome, Human, HeLa Cells, Histones, Humans, K562 Cells, Promoter Regions, Genetic, Transcription Factors
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.

DOI10.1038/nature07829
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/19295514?dopt=Abstract
PMCPMC2910248
Alternate JournalNature
PubMed ID19295514