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A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast

Author

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  • Hyelim Jo

    (Korea Advanced Institute of Science and Technology)

  • Taemook Kim

    (Korea Advanced Institute of Science and Technology)

  • Yujin Chun

    (Korea Advanced Institute of Science and Technology)

  • Inkyung Jung

    (Korea Advanced Institute of Science and Technology)

  • Daeyoup Lee

    (Korea Advanced Institute of Science and Technology)

Abstract

We herein employ in situ Hi-C with an auxin-inducible degron (AID) system to examine the effect of chromatin remodeling on 3D genome organization in yeast. Eight selected ATP-dependent chromatin remodelers representing various subfamilies contribute to 3D genome organization differently. Among the studied remodelers, the temporary depletions of Chd1p, Swr1p, and Sth1p (a catalytic subunit of the Remodeling the Structure of Chromatin [RSC] complex) cause the most significant defects in intra-chromosomal contacts, and the regulatory roles of these three remodelers in 3D genome organization differ depending on the chromosomal context and cell cycle stage. Furthermore, even though Chd1p and Isw1p are known to share functional similarities/redundancies, their depletions lead to distinct effects on 3D structures. The RSC and cohesin complexes also differentially modulate 3D genome organization within chromosome arm regions, whereas RSC appears to support the function of cohesin in centromeric clustering at G2 phase. Our work suggests that the ATP-dependent chromatin remodelers control the 3D genome organization of yeast through their chromatin-remodeling activities.

Suggested Citation

  • Hyelim Jo & Taemook Kim & Yujin Chun & Inkyung Jung & Daeyoup Lee, 2021. "A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26629-6
    DOI: 10.1038/s41467-021-26629-6
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    References listed on IDEAS

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    1. Zhijun Duan & Mirela Andronescu & Kevin Schutz & Sean McIlwain & Yoo Jung Kim & Choli Lee & Jay Shendure & Stanley Fields & C. Anthony Blau & William S. Noble, 2010. "A three-dimensional model of the yeast genome," Nature, Nature, vol. 465(7296), pages 363-367, May.
    2. Stephanie A. Schalbetter & Geoffrey Fudenberg & Jonathan Baxter & Katherine S. Pollard & Matthew J. Neale, 2019. "Principles of meiotic chromosome assembly revealed in S. cerevisiae," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    3. Iestyn Whitehouse & Andrew Flaus & Bradley R. Cairns & Malcolm F. White & Jerry L. Workman & Tom Owen-Hughes, 1999. "Nucleosome mobilization catalysed by the yeast SWI/SNF complex," Nature, Nature, vol. 400(6746), pages 784-787, August.
    4. Cyril Matthey-Doret & Lyam Baudry & Axel Breuer & Rémi Montagne & Nadège Guiglielmoni & Vittore Scolari & Etienne Jean & Arnaud Campeas & Philippe Henri Chanut & Edgar Oriol & Adrien Méot & Laurent Po, 2020. "Computer vision for pattern detection in chromosome contact maps," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
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