Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation

Liu, Yue1; Zhang, Zhihui1; Hu, Hongmiao2; Chen, Wei3; Zhang, Fan1; Wang, Qian1; Wang, Changshi1; Yan, Kaige4,5; Du, Jiamu1,5

2024-03-01

10.1038/s41477-024-01640-z

NATURE PLANTS   影响因子和分区

2055-026X

2055-0278

["Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers1. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components2-5. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation6-11. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeFx-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeFx-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.","Cryogenic electron microscopy structures of DDM1-nucleosome complexes in ADP-BeFx-bound, ADP-bound and nucleotide-free conformations reveal insights into the mechanism underlying chromatin remodelling by DDM1, a key chromatin remodeller involved in plant DNA methylation."]

SCI

英语

第一 ; 通讯

National Natural Science Foundation of China (National Science Foundation of China)[32325008] ; National Natural Science Foundation of China["RCJC20221008092720004","KQTD20190929173906742","20231120201445001"] ; Shenzhen Science and Technology Program[ALTF 579-2022]

Plant Sciences

Plant Sciences

WOS:001175678900001

NATURE PORTFOLIO

Web of Science

1.Southern Univ Sci & Technol, Key Lab Mol Design Plant Cell Factory, Inst Plant & Food Sci,Dept Biol, Sch Life Sci,Guangdong Higher Educ Inst, Shenzhen, Peoples R China
2.MRC Lab Mol Biol, Cambridge, England
3.Chinese Acad Sci, Shanghai Ctr Plant Stress Biol, CAS Ctr Excellence Mol Plant Sci, Shanghai, Peoples R China
4.Southern Univ Sci & Technol, Sch Life Sci, Dept Chem Biol, Shenzhen, Peoples R China
5.Southern Univ Sci & Technol, Inst Biol Electron Microscopy, Shenzhen, Peoples R China

Liu, Yue,Zhang, Zhihui,Hu, Hongmiao,et al. Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation[J]. NATURE PLANTS,2024,10(3).

Liu, Yue.,Zhang, Zhihui.,Hu, Hongmiao.,Chen, Wei.,Zhang, Fan.,...&Du, Jiamu.(2024).Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.NATURE PLANTS,10(3).

Liu, Yue,et al."Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation".NATURE PLANTS 10.3(2024).