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Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
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 recogn...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208443/ https://www.ncbi.nlm.nih.gov/pubmed/30382101 http://dx.doi.org/10.1038/s41467-018-06965-w |
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author | Zhang, Cuijun Du, Xuan Tang, Kai Yang, Zhenlin Pan, Li Zhu, Peipei Luo, Jinyan Jiang, Yuwei Zhang, Hui Wan, Huafang Wang, Xingang Wu, Fengkai Tao, W. Andy He, Xin-Jian Zhang, Heng Bressan, Ray A. Du, Jiamu Zhu, Jian-Kang |
author_facet | Zhang, Cuijun Du, Xuan Tang, Kai Yang, Zhenlin Pan, Li Zhu, Peipei Luo, Jinyan Jiang, Yuwei Zhang, Hui Wan, Huafang Wang, Xingang Wu, Fengkai Tao, W. Andy He, Xin-Jian Zhang, Heng Bressan, Ray A. Du, Jiamu Zhu, Jian-Kang |
author_sort | Zhang, Cuijun |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6208443 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-62084432018-10-31 Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin Zhang, Cuijun Du, Xuan Tang, Kai Yang, Zhenlin Pan, Li Zhu, Peipei Luo, Jinyan Jiang, Yuwei Zhang, Hui Wan, Huafang Wang, Xingang Wu, Fengkai Tao, W. Andy He, Xin-Jian Zhang, Heng Bressan, Ray A. Du, Jiamu Zhu, Jian-Kang Nat Commun Article 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. Nature Publishing Group UK 2018-10-31 /pmc/articles/PMC6208443/ /pubmed/30382101 http://dx.doi.org/10.1038/s41467-018-06965-w Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Zhang, Cuijun Du, Xuan Tang, Kai Yang, Zhenlin Pan, Li Zhu, Peipei Luo, Jinyan Jiang, Yuwei Zhang, Hui Wan, Huafang Wang, Xingang Wu, Fengkai Tao, W. Andy He, Xin-Jian Zhang, Heng Bressan, Ray A. Du, Jiamu Zhu, Jian-Kang Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin |
title | Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin |
title_full | Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin |
title_fullStr | Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin |
title_full_unstemmed | Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin |
title_short | Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin |
title_sort | arabidopsis agdp1 links h3k9me2 to dna methylation in heterochromatin |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208443/ https://www.ncbi.nlm.nih.gov/pubmed/30382101 http://dx.doi.org/10.1038/s41467-018-06965-w |
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