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Nature. 2015 Feb 19;518(7539):350-354. doi: 10.1038/nature14217.

Integrative analysis of haplotype-resolved epigenomes across human tissues.

Author information

1
Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
2
Department of Genetics, Stanford University, 300 Pasteur Drive, M-344 Stanford, California 94305, USA.
3
Department of Cardiovascular Medicine, Stanford University, Falk Building, 870 Quarry Road Stanford, California 94304, USA.
4
Department of Surgery, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8109, St. Louis, Missouri 63110, USA.
5
Tsinghua University-Peking University Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
6
Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA.
7
Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92093, USA.
8
Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas. NSERL, RL10, 800 W Campbell Road, Richardson, TX 75080.
9
Department of Medicine, Division of Cardiology, University of California, San Diego, CA 92093-0613J, USA.
10
Bioinformatics Division, Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, China.
11
Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
12
UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
#
Contributed equally

Abstract

Allelic differences between the two homologous chromosomes can affect the propensity of inheritance in humans; however, the extent of such differences in the human genome has yet to be fully explored. Here we delineate allelic chromatin modifications and transcriptomes among a broad set of human tissues, enabled by a chromosome-spanning haplotype reconstruction strategy. The resulting large collection of haplotype-resolved epigenomic maps reveals extensive allelic biases in both chromatin state and transcription, which show considerable variation across tissues and between individuals, and allow us to investigate cis-regulatory relationships between genes and their control sequences. Analyses of histone modification maps also uncover intriguing characteristics of cis-regulatory elements and tissue-restricted activities of repetitive elements. The rich data sets described here will enhance our understanding of the mechanisms by which cis-regulatory elements control gene expression programs.

PMID:
25693566
PMCID:
PMC4449149
DOI:
10.1038/nature14217
[Indexed for MEDLINE]
Free PMC Article

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