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Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

Author

Listed:
  • Cuijun Zhang

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    Purdue University)

  • Xuan Du

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Kai Tang

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    Purdue University)

  • Zhenlin Yang

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Li Pan

    (Purdue University)

  • Peipei Zhu

    (Purdue University)

  • Jinyan Luo

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Yuwei Jiang

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Hui Zhang

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Huafang Wan

    (Purdue University
    Southwest University)

  • Xingang Wang

    (Purdue University)

  • Fengkai Wu

    (Purdue University
    Sichuan Agricultural University)

  • W. Andy Tao

    (Purdue University)

  • Xin-Jian He

    (National Institute of Biological Sciences)

  • Heng Zhang

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Ray A. Bressan

    (Purdue University)

  • Jiamu Du

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Jian-Kang Zhu

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    Purdue University)

Abstract

Heterochromatin is a tightly packed form of chromatin that is associated with DNA methylation and histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2-binding protein, Agenet domain (AGD)-containing p1 (AGDP1), in Arabidopsis thaliana. Here we find that AGDP1 can specifically recognize the H3K9me2 mark by its three pairs of tandem AGDs. We determine the crystal structure of the Agenet domain 1 and 2 cassette (AGD12) of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 specifically recognizes the H3K4me0 and H3K9me2 marks by hydrogen bonding and hydrophobic interactions. In addition, we find that AGDP1 is required for transcriptional silencing, non-CG DNA methylation, and H3K9 dimethylation at some loci. ChIP-seq data show that AGDP1 preferentially occupies long transposons and is associated with heterochromatin marks. Our findings suggest that, as a heterochromatin-binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions.

Suggested Citation

  • Cuijun Zhang & Xuan Du & Kai Tang & Zhenlin Yang & Li Pan & Peipei Zhu & Jinyan Luo & Yuwei Jiang & Hui Zhang & Huafang Wan & Xingang Wang & Fengkai Wu & W. Andy Tao & Xin-Jian He & Heng Zhang & Ray A, 2018. "Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06965-w
    DOI: 10.1038/s41467-018-06965-w
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    Cited by:

    1. Jie Liu & Xuehua Zhong, 2024. "Epiallelic variation of non-coding RNA genes and their phenotypic consequences," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Jian Fang & Jianjun Jiang & Sarah M. Leichter & Jie Liu & Mahamaya Biswal & Nelli Khudaverdyan & Xuehua Zhong & Jikui Song, 2022. "Mechanistic basis for maintenance of CHG DNA methylation in plants," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Zsolt Karányi & Ágnes Mosolygó-L & Orsolya Feró & Adrienn Horváth & Beáta Boros-Oláh & Éva Nagy & Szabolcs Hetey & Imre Holb & Henrik Mihály Szaker & Márton Miskei & Tibor Csorba & Lóránt Székvölgyi, 2022. "NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis," Nature Communications, Nature, vol. 13(1), pages 1-20, December.

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