Human DNA methylomes at base resolution show widespread epigenomic differences

Ryan Lister, Mattia Pelizzola, Robert H. Dowen, R. David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R. Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo, Lee Edsall, Jessica Antosiewicz-Bourget, Ron Stewart, Victor Ruotti, A. Harvey Millar, James A. Thomson, Bing Ren and Joseph R. Ecker ()
Additional contact information
Ryan Lister: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
Mattia Pelizzola: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
Robert H. Dowen: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
R. David Hawkins: Ludwig Institute for Cancer Research,
Gary Hon: Ludwig Institute for Cancer Research,
Julian Tonti-Filippini: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia
Joseph R. Nery: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
Leonard Lee: Ludwig Institute for Cancer Research,
Zhen Ye: Ludwig Institute for Cancer Research,
Que-Minh Ngo: Ludwig Institute for Cancer Research,
Lee Edsall: Ludwig Institute for Cancer Research,
Jessica Antosiewicz-Bourget: Morgridge Institute for Research, Madison, Wisconsin 53707, USA
Ron Stewart: Morgridge Institute for Research, Madison, Wisconsin 53707, USA
Victor Ruotti: Morgridge Institute for Research, Madison, Wisconsin 53707, USA
A. Harvey Millar: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia
James A. Thomson: Morgridge Institute for Research, Madison, Wisconsin 53707, USA
Bing Ren: Ludwig Institute for Cancer Research,
Joseph R. Ecker: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA

Nature, 2009, vol. 462, issue 7271, 315-322

Abstract: Abstract DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA–protein interaction for several key regulatory factors. Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes. Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that embryonic stem cells may use different methylation mechanisms to affect gene regulation. Methylation in non-CG contexts showed enrichment in gene bodies and depletion in protein binding sites and enhancers. Non-CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells. We identified hundreds of differentially methylated regions proximal to genes involved in pluripotency and differentiation, and widespread reduced methylation levels in fibroblasts associated with lower transcriptional activity. These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development.

Date: 2009
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DOI: 10.1038/nature08514

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