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

Publication ,  Journal Article
Heintzman, ND; Hon, GC; Hawkins, RD; Kheradpour, P; Stark, A; Harp, LF; Ye, Z; Lee, LK; Stuart, RK; Ching, CW; Ching, KA; Liu, H; Zhang, X ...
Published in: Nature
May 7, 2009

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.

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Published In

Nature

DOI

EISSN

1476-4687

Publication Date

May 7, 2009

Volume

459

Issue

7243

Start / End Page

108 / 112

Location

England

Related Subject Headings

  • Transcription Factors
  • Promoter Regions, Genetic
  • K562 Cells
  • Humans
  • Histones
  • Hela Cells
  • HeLa Cells
  • Genome, Human
  • General Science & Technology
  • Gene Expression Regulation
 

Citation

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ICMJE
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Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., … Ren, B. (2009). Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature, 459(7243), 108–112. https://doi.org/10.1038/nature07829
Heintzman, Nathaniel D., Gary C. Hon, R David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, et al. “Histone modifications at human enhancers reflect global cell-type-specific gene expression.Nature 459, no. 7243 (May 7, 2009): 108–12. https://doi.org/10.1038/nature07829.
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009 May 7;459(7243):108–12.
Heintzman, Nathaniel D., et al. “Histone modifications at human enhancers reflect global cell-type-specific gene expression.Nature, vol. 459, no. 7243, May 2009, pp. 108–12. Pubmed, doi:10.1038/nature07829.
Heintzman ND, Hon GC, Hawkins RD, 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. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009 May 7;459(7243):108–112.
Journal cover image

Published In

Nature

DOI

EISSN

1476-4687

Publication Date

May 7, 2009

Volume

459

Issue

7243

Start / End Page

108 / 112

Location

England

Related Subject Headings

  • Transcription Factors
  • Promoter Regions, Genetic
  • K562 Cells
  • Humans
  • Histones
  • Hela Cells
  • HeLa Cells
  • Genome, Human
  • General Science & Technology
  • Gene Expression Regulation