title: Integrative analysis of haplotype-resolved epigenomes across human tissues.
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.
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Danny
authors.initials: D
authors.lastname: Leung
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Inkyung
authors.initials: I
authors.lastname: Jung
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Nisha
authors.initials: N
authors.lastname: Rajagopal
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Anthony
authors.initials: A
authors.lastname: Schmitt
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Siddarth
authors.initials: S
authors.lastname: Selvaraj
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Ah Young
authors.initials: AY
authors.lastname: Lee
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Chia-An
authors.initials: CA
authors.lastname: Yen
authors.affiliation: Department of Genetics, Stanford University, 300 Pasteur Drive, M-344 Stanford, California 94305, USA.|Department of Cardiovascular Medicine, Stanford University, Falk Building, 870 Quarry Road Stanford, California 94304, USA.|Department of Surgery, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8109, St. Louis, Missouri 63110, USA.
authors.forename: Shin
authors.initials: S
authors.lastname: Lin
authors.affiliation: Department of Genetics, Stanford University, 300 Pasteur Drive, M-344 Stanford, California 94305, USA.|Department of Cardiovascular Medicine, Stanford University, Falk Building, 870 Quarry Road Stanford, California 94304, USA.|Department of Surgery, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8109, St. Louis, Missouri 63110, USA.
authors.forename: Yiing
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Yunjiang
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.|Tsinghua University-Peking University Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Xie
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.|Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Yue
authors.affiliation: Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92093, USA.
authors.forename: Manoj
authors.initials: M
authors.lastname: Hariharan
authors.affiliation: Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas. NSERL, RL10, 800 W Campbell Road, Richardson, TX 75080.
authors.forename: Pradipta
authors.initials: P
authors.lastname: Ray
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Samantha
authors.initials: S
authors.lastname: Kuan
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
authors.forename: Lee
authors.initials: L
authors.lastname: Edsall
authors.affiliation: Department of Medicine, Division of Cardiology, University of California, San Diego, CA 92093-0613J, USA.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Yang
authors.affiliation: Department of Medicine, Division of Cardiology, University of California, San Diego, CA 92093-0613J, USA.
authors.forename: Neil C
authors.initials: NC
authors.lastname: Chi
authors.affiliation: Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas. NSERL, RL10, 800 W Campbell Road, Richardson, TX 75080.|Bioinformatics Division, Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, China.
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
authors.affiliation: Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92093, USA.|Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
authors.affiliation: Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.|Department of Medicine, Division of Cardiology, University of California, San Diego, CA 92093-0613J, USA.|UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: Ren
mesh_terms: D000107:Acetylation; D000483:Alleles; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D002877:Chromosomes, Human / Q000235:genetics; D066264:Datasets as Topic; D004742:Enhancer Elements, Genetic / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics*; D057890:Epigenomics; D014644:Genetic Variation / Q000235:genetics; D006239:Haplotypes / Q000235:genetics*; D006657:Histones / Q000378:metabolism; D006801:Humans; D059372:Nucleotide Motifs; D009928:Organ Specificity / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D002843:Chromatin; D006657:Histones