Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
Structure. 2024 Aug 8;32(8):1222-1230.e4. doi: 10.1016/j.str.2024.05.013. Epub 2024 Jun 12.
The SWI/SNF2 chromatin remodeling factor decreased DNA methylation 1 (DDM1) is essential for the silencing of transposable elements (TEs) in both euchromatic and heterochromatic regions. Here, we determined the cryo-EM structures of DDM1-nucleosome and DDM1-nucleosome complexes at near-atomic resolution in the presence of the ATP analog ADP-BeFx. The structures show that nucleosomal DNA is unwrapped more on the surface of the histone octamer containing histone H2A than that containing histone H2A.W. DDM1 embraces one DNA gyre of the nucleosome and interacts with the N-terminal tails of histone H4. Although we did not observe DDM1-H2A.W interactions in our structures, the results of the pull-down experiments suggest a direct interaction between DDM1 and the core region of histone H2A.W. Our work provides mechanistic insights into the heterochromatin remodeling process driven by DDM1 in plants.
SWI/SNF2 染色质重塑因子降低 DNA 甲基化 1（DDM1）对于常染色质和异染色质区域中转座元件（TEs）的沉默是必不可少的。在这里，我们在存在 ATP 类似物 ADP-BeFx 的情况下，以近原子分辨率确定了 DDM1-核小体和 DDM1-核小体复合物的冷冻电镜结构。这些结构表明，核小体 DNA 在含有组蛋白 H2A 的组蛋白八聚体表面上的展开程度大于含有组蛋白 H2A.W 的展开程度。DDM1 环抱核小体的一个 DNA 旋圈，并与组蛋白 H4 的 N 端尾巴相互作用。尽管我们在结构中没有观察到 DDM1-H2A.W 相互作用，但下拉实验的结果表明 DDM1 与组蛋白 H2A.W 的核心区域之间存在直接相互作用。我们的工作为植物中由 DDM1 驱动的异染色质重塑过程提供了机制见解。
