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Integrative analysis of haplotype-resolved epigenomes across human tissues

Author

Listed:
  • Danny Leung

    (Ludwig Institute for Cancer Research)

  • Inkyung Jung

    (Ludwig Institute for Cancer Research)

  • Nisha Rajagopal

    (Ludwig Institute for Cancer Research)

  • Anthony Schmitt

    (Ludwig Institute for Cancer Research)

  • Siddarth Selvaraj

    (Ludwig Institute for Cancer Research)

  • Ah Young Lee

    (Ludwig Institute for Cancer Research)

  • Chia-An Yen

    (Ludwig Institute for Cancer Research)

  • Shin Lin

    (Stanford University, 300 Pasteur Drive, M-344 Stanford, California 94305, USA
    Stanford University, Falk Building, 870 Quarry Road Stanford, California 94304, USA)

  • Yiing Lin

    (Stanford University, 300 Pasteur Drive, M-344 Stanford, California 94305, USA
    Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8109)

  • Yunjiang Qiu

    (Ludwig Institute for Cancer Research)

  • Wei Xie

    (Tsinghua University–Peking University Center for Life Sciences, School of Life Sciences, Tsinghua University)

  • Feng Yue

    (College of Medicine, The Pennsylvania State University)

  • Manoj Hariharan

    (Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies)

  • Pradipta Ray

    (Biological Sciences, Center for Systems Biology, The University of Texas at Dallas)

  • Samantha Kuan

    (Ludwig Institute for Cancer Research)

  • Lee Edsall

    (Ludwig Institute for Cancer Research)

  • Hongbo Yang

    (University of California)

  • Neil C. Chi

    (University of California
    Institute of Genomic Medicine, University of California)

  • Michael Q. Zhang

    (Biological Sciences, Center for Systems Biology, The University of Texas at Dallas
    Center for Synthetic and Systems Biology, TNLIST Tsinghua National Laboratory for Information Science and Technology, Tsinghua University)

  • Joseph R. Ecker

    (Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies)

  • Bing Ren

    (Ludwig Institute for Cancer Research
    Institute of Genomic Medicine, University of California
    University of California San Diego
    UCSD Moores Cancer Center, University of California San Diego)

Abstract

As part of the Epigenome Roadmap project, this study uses a chromosome-spanning haplotype reconstruction strategy to construct haplotype-resolved epigenomic maps for a diverse set of human tissues; the maps reveal extensive allelic biases in chromatin state and transcription, which vary across individuals due to genetic backgrounds.

Suggested Citation

  • Danny Leung & Inkyung Jung & Nisha Rajagopal & Anthony Schmitt & Siddarth Selvaraj & Ah Young Lee & Chia-An Yen & Shin Lin & Yiing Lin & Yunjiang Qiu & Wei Xie & Feng Yue & Manoj Hariharan & Pradipta , 2015. "Integrative analysis of haplotype-resolved epigenomes across human tissues," Nature, Nature, vol. 518(7539), pages 350-354, February.
    • Handle: RePEc:nat:nature:v:518:y:2015:i:7539:d:10.1038_nature14217
    DOI: 10.1038/nature14217
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    Cited by:

    1. Peter H. Dixon & Adam P. Levine & Inês Cebola & Melanie M. Y. Chan & Aliya S. Amin & Anshul Aich & Monika Mozere & Hannah Maude & Alice L. Mitchell & Jun Zhang & Jenny Chambers & Argyro Syngelaki & Je, 2022. "GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Ting Shen & Ting Ni & Jiaxuan Chen & Haitao Chen & Xiaopin Ma & Guangwen Cao & Tianzhi Wu & Haisheng Xie & Bin Zhou & Gang Wei & Hexige Saiyin & Suqin Shen & Peng Yu & Qianyi Xiao & Hui Liu & Yuzheng , 2022. "An enhancer variant at 16q22.1 predisposes to hepatocellular carcinoma via regulating PRMT7 expression," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Zhaohui Qin & Ben Li & Karen N. Conneely & Hao Wu & Ming Hu & Deepak Ayyala & Yongseok Park & Victor X. Jin & Fangyuan Zhang & Han Zhang & Li Li & Shili Lin, 2016. "Statistical Challenges in Analyzing Methylation and Long-Range Chromosomal Interaction Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 8(2), pages 284-309, October.
    4. Andrea Wilderman & Eva D’haene & Machteld Baetens & Tara N. Yankee & Emma Wentworth Winchester & Nicole Glidden & Ellen Roets & Jo Dorpe & Sandra Janssens & Danny E. Miller & Miranda Galey & Kari M. B, 2024. "A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development," Nature Communications, Nature, vol. 15(1), pages 1-23, December.

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