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

Nathaniel D. Heintzman, Gary C. Hon, R. David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, Leonard K. Lee, Rhona K. Stuart, Christina W. Ching, Keith A. Ching, Jessica E. Antosiewicz-Bourget, Hui Liu, Xinmin Zhang, Roland D. Green, Victor V. Lobanenkov, Ron Stewart, James A. Thomson, Gregory E. Crawford, Manolis Kellis and Bing Ren ()
Additional contact information
Nathaniel D. Heintzman: Ludwig Institute for Cancer Research,
Gary C. Hon: Ludwig Institute for Cancer Research,
R. David Hawkins: Ludwig Institute for Cancer Research,
Pouya Kheradpour: MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar Street, Cambridge, Massachusetts 02139, USA
Alexander Stark: MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar Street, Cambridge, Massachusetts 02139, USA
Lindsey F. Harp: Ludwig Institute for Cancer Research,
Zhen Ye: Ludwig Institute for Cancer Research,
Leonard K. Lee: Ludwig Institute for Cancer Research,
Rhona K. Stuart: Ludwig Institute for Cancer Research,
Christina W. Ching: Ludwig Institute for Cancer Research,
Keith A. Ching: Ludwig Institute for Cancer Research,
Jessica E. Antosiewicz-Bourget: Morgridge Institute for Research, Madison, Wisconsin 53707-7365, USA
Hui Liu: Roche NimbleGen, Inc., 500 South Rosa Road, Madison, Wisconsin 53719, USA
Xinmin Zhang: Roche NimbleGen, Inc., 500 South Rosa Road, Madison, Wisconsin 53719, USA
Roland D. Green: Roche NimbleGen, Inc., 500 South Rosa Road, Madison, Wisconsin 53719, USA
Victor V. Lobanenkov: National Institutes of Allergy and Infectious Disease, 5640 Fishers Lane, Rockville, Maryland 20852, USA
Ron Stewart: Morgridge Institute for Research, Madison, Wisconsin 53707-7365, USA
James A. Thomson: Morgridge Institute for Research, Madison, Wisconsin 53707-7365, USA
Gregory E. Crawford: Institute for Genome Sciences and Policy, Duke University, 101 Science Drive, Durham, North Carolina 27708, USA
Manolis Kellis: MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar Street, Cambridge, Massachusetts 02139, USA
Bing Ren: Ludwig Institute for Cancer Research,

Nature, 2009, vol. 459, issue 7243, 108-112

Abstract: Gene enhancers on the map The relative role of promoters, enhancers and other regulatory DNA elements in determining cell-type-specific gene expression is poorly understood. Now a chromatin-immunoprecipitation-based microarray (ChIP-chip) method has been used to generate maps of histone modifications at promoters and enhancers in several different human cell lines. The modification patterns at promoters are found to be largely invariant between cell types, whereas the patterns at most enhancers are specific to a single cell type and correlate with cell-type-specific gene expression.

Date: 2009
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DOI: 10.1038/nature07829

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