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H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots

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  • Xiaochang Yin

    (Peking University)

  • Francisco J. Romero-Campero

    (Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC)
    Department of Computer Science and Artificial Intelligence (University of Sevilla))

  • Pedro de Los Reyes

    (Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC))

  • Peng Yan

    (Zhejiang University)

  • Jing Yang

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Guangmei Tian

    (Peking University)

  • XiaoZeng Yang

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Xiaorong Mo

    (Zhejiang University)

  • Shuangshuang Zhao

    (Shandong Normal University)

  • Myriam Calonje

    (Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC))

  • Yue Zhou

    (Peking University)

Abstract

Although it is well established that the Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin accessibility, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that PcG function regulates chromatin accessibility. We find that H2AK121ub is associated with a less accessible but still permissive chromatin at transcriptional regulation hotspots. Accessibility is further reduced by EMF1 acting in collaboration with PRC2 activity. Consequently, H2AK121ub/H3K27me3 marks are linked to inaccessible although responsive chromatin. In contrast, only-H3K27me3-marked chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Nevertheless, despite the loss of PcG activities leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that accessible chromatin is not always predictive of gene expression.

Suggested Citation

  • Xiaochang Yin & Francisco J. Romero-Campero & Pedro de Los Reyes & Peng Yan & Jing Yang & Guangmei Tian & XiaoZeng Yang & Xiaorong Mo & Shuangshuang Zhao & Myriam Calonje & Yue Zhou, 2021. "H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20614-1
    DOI: 10.1038/s41467-020-20614-1
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    Cited by:

    1. James Godwin & Mohan Govindasamy & Kiruba Nedounsejian & Eduardo March & Ronan Halton & Clara Bourbousse & Léa Wolff & Antoine Fort & Michal Krzyszton & Jesús López Corrales & Szymon Swiezewski & Fred, 2024. "The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Yu Zhang & Min Ma & Meng Liu & Aiqing Sun & Xiaoyun Zheng & Kunpeng Liu & Chunmei Yin & Chuanshun Li & Cizhong Jiang & Xiaoyu Tu & Yuda Fang, 2023. "Histone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Pawel Mikulski & Philip Wolff & Tiancong Lu & Mathias Nielsen & Elsa Franco Echevarria & Danling Zhu & Julia I. Questa & Gerhard Saalbach & Carlo Martins & Caroline Dean, 2022. "VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. Linhua Sun & Jingru Zhou & Xiao Xu & Yi Liu & Ni Ma & Yutong Liu & Wenchao Nie & Ling Zou & Xing Wang Deng & Hang He, 2024. "Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    5. Chih-Hung Hsieh & Ya-Ting Sabrina Chang & Ming-Ren Yen & Jo-Wei Allison Hsieh & Pao-Yang Chen, 2024. "Predicting protein synergistic effect in Arabidopsis using epigenome profiling," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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