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

@article{citeulike:4200583, 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 gene1, 2, 3, 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 genome4, 5, 6. 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.}, author = {Heintzman, Nathaniel D. and Hon, Gary C. and Hawkins, R. David and Kheradpour, Pouya and Stark, Alexander and Harp, Lindsey F. and Ye, Zhen and Lee, Leonard K. and Stuart, Rhona K. and Ching, Christina W. and Ching, Keith A. and Antosiewicz-Bourget, Jessica E. and Liu, Hui and Zhang, Xinmin and Green, Roland D. and Lobanenkov, Victor V. and Stewart, Ron and Thomson, James A. and Crawford, Gregory E. and Kellis, Manolis and Ren, Bing}, citeulike-article-id = {4200583}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature07829}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature07829}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19295514}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19295514}, day = {18}, doi = {10.1038/nature07829}, issn = {0028-0836}, journal = {Nature}, keywords = {2009, clip-chip, enhancers, expression, histone\_modification, histones, insulators}, month = {March}, number = {7243}, pages = {108--112}, posted-at = {2009-11-12 03:15:39}, priority = {5}, publisher = {Nature Publishing Group}, title = {Histone modifications at human enhancers reflect global cell-type-specific gene expression}, url = {http://dx.doi.org/10.1038/nature07829}, volume = {459}, year = {2009} }

TY - JOUR ID - citeulike:4200583 L3 - citeulike-article-id:4200583 N2 - 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 gene1, 2, 3, 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 genome4, 5, 6. 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. IS - 7243 JF - Nature SN - 0028-0836 EP - 112 TI - Histone modifications at human enhancers reflect global cell-type-specific gene expression PB - Nature Publishing Group VL - 459 SP - 108 KW - 2009 KW - clip-chip KW - enhancers KW - expression KW - histone_modification KW - histones KW - insulators AU - Heintzman, Nathaniel AU - Hon, Gary AU - Hawkins, David AU - Kheradpour, Pouya AU - Stark, Alexander AU - Harp, Lindsey AU - Ye, Zhen AU - Lee, Leonard AU - Stuart, Rhona AU - Ching, Christina AU - Ching, Keith AU - Antosiewicz-Bourget, Jessica AU - Liu, Hui AU - Zhang, Xinmin AU - Green, Roland AU - Lobanenkov, Victor AU - Stewart, Ron AU - Thomson, James AU - Crawford, Gregory AU - Kellis, Manolis AU - Ren, Bing PY - 2009/03/18/ UR - http://dx.doi.org/10.1038/nature07829 ER -