Publication Date:
2015-02-20
Description:
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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449149/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449149/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leung, Danny -- Jung, Inkyung -- Rajagopal, Nisha -- Schmitt, Anthony -- Selvaraj, Siddarth -- Lee, Ah Young -- Yen, Chia-An -- Lin, Shin -- Lin, Yiing -- Qiu, Yunjiang -- Xie, Wei -- Yue, Feng -- Hariharan, Manoj -- Ray, Pradipta -- Kuan, Samantha -- Edsall, Lee -- Yang, Hongbo -- Chi, Neil C -- Zhang, Michael Q -- Ecker, Joseph R -- Ren, Bing -- ES017166/ES/NIEHS NIH HHS/ -- F32 HL110473/HL/NHLBI NIH HHS/ -- F32HL110473/HL/NHLBI NIH HHS/ -- K99 HL119617/HL/NHLBI NIH HHS/ -- K99HL119617/HL/NHLBI NIH HHS/ -- R01 ES024984/ES/NIEHS NIH HHS/ -- T32 GM008666/GM/NIGMS NIH HHS/ -- U01 ES017166/ES/NIEHS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Feb 19;518(7539):350-4. doi: 10.1038/nature14217.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ludwig Institute for Cancer Research, La Jolla, California 92093, USA. ; 1] Department of Genetics, Stanford University, 300 Pasteur Drive, M-344 Stanford, California 94305, USA [2] Department of Cardiovascular Medicine, Stanford University, Falk Building, 870 Quarry Road Stanford, California 94304, USA. ; 1] Department of Genetics, Stanford University, 300 Pasteur Drive, M-344 Stanford, California 94305, USA [2] Department of Surgery, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8109, St Louis, Missouri 63110, USA. ; Tsinghua University-Peking University Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. ; Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA. ; Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92093, USA. ; Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA. ; Department of Medicine, Division of Cardiology, University of California, San Diego, California 92093-0613, USA. ; 1] Department of Medicine, Division of Cardiology, University of California, San Diego, California 92093-0613, USA [2] Institute of Genomic Medicine, University of California, San Diego, California 92093, USA. ; 1] Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA [2] Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing 100084, China. ; 1] Ludwig Institute for Cancer Research, La Jolla, California 92093, USA [2] Institute of Genomic Medicine, University of California, San Diego, California 92093, USA [3] Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA [4] UCSD Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25693566" target="_blank"〉PubMed〈/a〉
Keywords:
Acetylation
;
*Alleles
;
Chromatin/genetics/metabolism
;
Chromosomes, Human/genetics
;
Datasets as Topic
;
Enhancer Elements, Genetic/genetics
;
Epigenesis, Genetic/*genetics
;
*Epigenomics
;
Genetic Variation/genetics
;
Haplotypes/*genetics
;
Histones/metabolism
;
Humans
;
Nucleotide Motifs
;
Organ Specificity/genetics
;
Transcription, Genetic/genetics
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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