@article{d6af1f70047940a0bf59c597c44c36c1,
title = "Human body epigenome maps reveal noncanonical DNA methylation variation",
abstract = "Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual{\^a} €{\texttrademark} s cells, with epigenetic mechanisms that could have tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals{\^a} €{\texttrademark} phased genome, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in several genomic contexts varies substantially among human tissues.",
author = "Schultz, {Matthew D.} and Yupeng He and Whitaker, {John W.} and Manoj Hariharan and Mukamel, {Eran A.} and Danny Leung and Nisha Rajagopal and Nery, {Joseph R.} and Urich, {Mark A.} and Huaming Chen and Shin Lin and Yiing Lin and Inkyung Jung and Schmitt, {Anthony D.} and Siddarth Selvaraj and Bing Ren and Sejnowski, {Terrence J.} and Wei Wang and Ecker, {Joseph R.}",
note = "Funding Information: Acknowledgements We thank R. J. Schmitz for critical reading of the manuscript. This work is supported by the National Institutes of Health (NIH) Epigenome Roadmap Project (U01 ES017166). E.A.M. was supported by National Institute of Neurological Diseases and Stroke grant (R00NS080911). J.R.E. was supported by the Gordon and Betty Moore Foundation (GMBF3034) and the Mary K. Chapman Foundation. T.J.S. and J.R.E. are investigators of the Howard Hughes Medical Institute. S.L. was supported by NIH fellowship grants F32HL110473 and K99HL119617. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing HPC resources that have contributed to the research results reported within this paper. The authors would also like to thank Mid-America Transplant Services, St Louis, for their support of this research effort.",
year = "2015",
month = jul,
day = "9",
doi = "10.1038/nature14465",
language = "English",
volume = "523",
pages = "212--216",
journal = "Nature",
issn = "0028-0836",
number = "7559",
}