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拟南芥 DDM1 的染色质重塑活性的分子和结构基础。

Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.

机构信息

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.

出版信息

Nat Commun. 2024 Jul 11;15(1):5187. doi: 10.1038/s41467-024-49465-w.

DOI:10.1038/s41467-024-49465-w
PMID:38992002
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11239853/
Abstract

The histone H2A variant H2A.W occupies transposons and thus prevents access to them in Arabidopsis thaliana. H2A.W is deposited by the chromatin remodeler DDM1, which also promotes the accessibility of chromatin writers to heterochromatin by an unknown mechanism. To shed light on this question, we solve the cryo-EM structures of nucleosomes containing H2A and H2A.W, and the DDM1-H2A.W nucleosome complex. These structures show that the DNA end flexibility of the H2A nucleosome is higher than that of the H2A.W nucleosome. In the DDM1-H2A.W nucleosome complex, DDM1 binds to the N-terminal tail of H4 and the nucleosomal DNA and increases the DNA end flexibility of H2A.W nucleosomes. Based on these biochemical and structural results, we propose that DDM1 counters the low accessibility caused by nucleosomes containing H2A.W to enable the maintenance of repressive epigenetic marks on transposons and prevent their activity.

摘要

组蛋白 H2A 变体 H2A.W 占据转座子，从而阻止其在拟南芥中的进入。H2A.W 由染色质重塑因子 DDM1 沉积，后者还通过未知机制促进染色质 writers 对异染色质的可及性。为了解决这个问题，我们解析了含有 H2A 和 H2A.W 的核小体以及 DDM1-H2A.W 核小体复合物的低温电镜结构。这些结构表明，H2A 核小体的 DNA 末端灵活性高于 H2A.W 核小体。在 DDM1-H2A.W 核小体复合物中，DDM1 结合到 H4 的 N 端尾巴和核小体 DNA 上，并增加了 H2A.W 核小体的 DNA 末端灵活性。基于这些生化和结构结果，我们提出 DDM1 可以抵消由含有 H2A.W 的核小体引起的低可及性，从而维持转座子上的抑制性表观遗传标记，并防止其活性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/0e0be41b9665/41467_2024_49465_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/489a5c4e69ea/41467_2024_49465_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/b7d24329b835/41467_2024_49465_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/a0c6e4712dce/41467_2024_49465_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/9abdfd281b67/41467_2024_49465_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/5635a870c91f/41467_2024_49465_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/fbe69cf2f849/41467_2024_49465_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/4e002d89cb13/41467_2024_49465_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/0e0be41b9665/41467_2024_49465_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/489a5c4e69ea/41467_2024_49465_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/b7d24329b835/41467_2024_49465_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/a0c6e4712dce/41467_2024_49465_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/9abdfd281b67/41467_2024_49465_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/5635a870c91f/41467_2024_49465_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/fbe69cf2f849/41467_2024_49465_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/4e002d89cb13/41467_2024_49465_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82b4/11239853/0e0be41b9665/41467_2024_49465_Fig8_HTML.jpg

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