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Chromatin architecture reorganization during stem cell differentiation

Author

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  • Jesse R. Dixon

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive
    Medical Scientist Training Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA)

  • Inkyung Jung

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Siddarth Selvaraj

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive
    Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA)

  • Yin Shen

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Jessica E. Antosiewicz-Bourget

    (The Morgridge Institute for Research, 309 North Orchard Street)

  • Ah Young Lee

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Zhen Ye

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Audrey Kim

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Nisha Rajagopal

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Wei Xie

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

  • Yarui Diao

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Jing Liang

    (University of Illinois at Urbana-Champaign)

  • Huimin Zhao

    (University of Illinois at Urbana-Champaign)

  • Victor V. Lobanenkov

    (Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Twinbrook I NIAID Facility, Room 1417, 5640 Fishers Lane, Rockville, Maryland 20852, USA)

  • Joseph R. Ecker

    (Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA)

  • James A. Thomson

    (The Morgridge Institute for Research, 309 North Orchard Street
    University of Wisconsin School of Medicine and Public Health
    Cellular, and Developmental Biology, University of California Santa Barbara)

  • Bing Ren

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive
    University of California, San Diego School of Medicine, Institute of Genomic Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

Abstract

Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.

Suggested Citation

  • Jesse R. Dixon & Inkyung Jung & Siddarth Selvaraj & Yin Shen & Jessica E. Antosiewicz-Bourget & Ah Young Lee & Zhen Ye & Audrey Kim & Nisha Rajagopal & Wei Xie & Yarui Diao & Jing Liang & Huimin Zhao , 2015. "Chromatin architecture reorganization during stem cell differentiation," Nature, Nature, vol. 518(7539), pages 331-336, February.
  • Handle: RePEc:nat:nature:v:518:y:2015:i:7539:d:10.1038_nature14222
    DOI: 10.1038/nature14222
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