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Structural and spatial chromatin features at developmental gene loci in human pluripotent stem cells

Author

Listed:
  • Hiroki Ikeda

    (Center for iPS Cell Research and Application (CiRA), Kyoto University)

  • Masamitsu Sone

    (Center for iPS Cell Research and Application (CiRA), Kyoto University
    Kyoto University)

  • Shinya Yamanaka

    (Center for iPS Cell Research and Application (CiRA), Kyoto University
    Gladstone Institute of Cardiovascular Disease)

  • Takuya Yamamoto

    (Center for iPS Cell Research and Application (CiRA), Kyoto University
    Kyoto University
    AMED-CREST, AMED 1-7-1 Otemach)

Abstract

Higher-order chromatin organization controls transcriptional programs that govern cell properties and functions. In order for pluripotent stem cells (PSCs) to appropriately respond to differentiation signals, developmental gene loci should be structurally and spatially regulated to be readily available for immediate transcription, even though these genes are hardly expressed in PSCs. Here, we show that both chromatin interaction profiles and nuclear positions at developmental gene loci differ between human somatic cells and hPSCs, and that changes in the chromatin interactions are closely related to the nuclear repositioning. Moreover, we also demonstrate that developmental gene loci, which have bivalent histone modifications, tend to colocalize in PSCs. Furthermore, this colocalization requires PRC1, PRC2, and TrxG complexes, which are essential regulatory factors for the maintenance of transcriptionally poised developmental genes. Our results indicate that higher-order chromatin regulation may be an integral part of the differentiation capacity that defines pluripotency.

Suggested Citation

  • Hiroki Ikeda & Masamitsu Sone & Shinya Yamanaka & Takuya Yamamoto, 2017. "Structural and spatial chromatin features at developmental gene loci in human pluripotent stem cells," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-01679-x
    DOI: 10.1038/s41467-017-01679-x
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