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

Author

Listed:
  • Nathaniel D. Heintzman

    (Ludwig Institute for Cancer Research,
    Biomedical Sciences Graduate Program,)

  • Gary C. Hon

    (Ludwig Institute for Cancer Research,
    Bioinformatics Program, and,)

  • 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
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, 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
    University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, 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
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Bing Ren

    (Ludwig Institute for Cancer Research,
    UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

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.

Suggested Citation

  • 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 & Jess, 2009. "Histone modifications at human enhancers reflect global cell-type-specific gene expression," Nature, Nature, vol. 459(7243), pages 108-112, May.
    • Handle: RePEc:nat:nature:v:459:y:2009:i:7243:d:10.1038_nature07829
    DOI: 10.1038/nature07829
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    Citations

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    Cited by:

    1. Christopher G Bell & Sarah Finer & Cecilia M Lindgren & Gareth A Wilson & Vardhman K Rakyan & Andrew E Teschendorff & Pelin Akan & Elia Stupka & Thomas A Down & Inga Prokopenko & Ian M Morison & Jonat, 2010. "Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus," PLOS ONE, Public Library of Science, vol. 5(11), pages 1-12, November.
    2. Xiaofeng Dai & Wenwen Guo & Chunjun Zhan & Xiuxia Liu & Zhonghu Bai & Yankun Yang, 2015. "WDR5 Expression Is Prognostic of Breast Cancer Outcome," PLOS ONE, Public Library of Science, vol. 10(9), pages 1-15, September.
    3. van Iterson Maarten & Duijkers Floor A.M. & Meijerink Jules P.P. & Admiraal Pieter & van Ommen Gert-Jan B. & Boer Judith M. & van Noesel Max M. & Menezes Renee X., 2012. "A Novel and Fast Normalization Method for High-Density Arrays," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(4), pages 1-31, July.
    4. Jingting Xu & Hong Hu & Yang Dai, 2016. "LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines," PLOS ONE, Public Library of Science, vol. 11(9), pages 1-18, September.
    5. Ian C McDowell & Dinesh Manandhar & Christopher M Vockley & Amy K Schmid & Timothy E Reddy & Barbara E Engelhardt, 2018. "Clustering gene expression time series data using an infinite Gaussian process mixture model," PLOS Computational Biology, Public Library of Science, vol. 14(1), pages 1-27, January.

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