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Nat Commun. 2018 Oct 31;9(1):4547. doi: 10.1038/s41467-018-06965-w.

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin.

Author information

1
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602, Shanghai, China.
2
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
3
University of Chinese Academy of Sciences, 100049, Beijing, China.
4
Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA.
5
College of Agronomy and Biotechnology, Southwest University, 400715, Chongqing, China.
6
Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China.
7
National Institute of Biological Sciences, 102206, Beijing, China.
8
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602, Shanghai, China. jmdu@sibs.ac.cn.
9
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602, Shanghai, China. jkzhu@sibs.ac.cn.
10
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA. jkzhu@sibs.ac.cn.

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.

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