Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

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. Bressan, Jiamu Du () and Jian-Kang Zhu ()
Additional contact information
Cuijun Zhang: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Xuan Du: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Kai Tang: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Zhenlin Yang: Shanghai Institutes for Biological Sciences, 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
Xingang Wang: Purdue University
Fengkai Wu: Purdue 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

Nature Communications, 2018, vol. 9, issue 1, 1-14

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-06965-w

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