ジャーナル: Cell / 年: 2023 タイトル: Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. 著者: Seung Cho Lee / Dexter W Adams / Jonathan J Ipsaro / Jonathan Cahn / Jason Lynn / Hyun-Soo Kim / Benjamin Berube / Viktoria Major / Joseph P Calarco / Chantal LeBlanc / Sonali Bhattacharjee / ...著者: Seung Cho Lee / Dexter W Adams / Jonathan J Ipsaro / Jonathan Cahn / Jason Lynn / Hyun-Soo Kim / Benjamin Berube / Viktoria Major / Joseph P Calarco / Chantal LeBlanc / Sonali Bhattacharjee / Umamaheswari Ramu / Daniel Grimanelli / Yannick Jacob / Philipp Voigt / Leemor Joshua-Tor / Robert A Martienssen / 要旨: Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 ...Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 promotes replacement of histone variant H3.3 by H3.1. In ddm1 mutants, DNA methylation is partly restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals engagement with histone H3.3 near residues required for assembly and with the unmodified H4 tail. An N-terminal autoinhibitory domain inhibits activity, while a disulfide bond in the helicase domain supports activity. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1, but is blocked by H4K16 acetylation. The male germline H3.3 variant MGH3/HTR10 is resistant to remodeling by DDM1 and acts as a placeholder nucleosome in sperm cells for epigenetic inheritance.
全体 : Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with ...
全体
名称: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
要素
複合体: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
複合体: DDM1
タンパク質・ペプチド: ATP-dependent DNA helicase DDM1
複合体: Nucleosome core particle
複合体: Histone octamer
タンパク質・ペプチド: Probable histone H2A.7
タンパク質・ペプチド: Histone H2B
タンパク質・ペプチド: Histone H3.3
タンパク質・ペプチド: Histone H4
複合体: DNA double helix
DNA: DNA (sense strand)
DNA: DNA (antisense strand)
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超分子 #1: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with ...
超分子
名称: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA) タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: Complex contains two copies of each histone (H2A.W, H2B, H3.3, and H4), 147 base pairs of DNA, and 1 copy of Arabidopsis DDM1
名称: Nucleosome core particle / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #1-#4, #6-#7 詳細: Complex contains two copies of each histone (H2A.W, H2B, H3.3, and H4) and 147 base pairs of DNA
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超分子 #4: Histone octamer
超分子
名称: Histone octamer / タイプ: complex / ID: 4 / 親要素: 3 / 含まれる分子: #1-#4 詳細: Contains two copies each of H2A.W, H2B, H3.3, and H4
凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 298 K / 装置: LEICA EM GP / 詳細: Blotted for 2.5 seconds before plunging..
詳細
DDM1 and reconstituted nucleosomes were reconstituted in a 4:1 molar ratio. Crosslinking with 0.05% glutaraldehyde was performed for 15 minutes followed by quenching with 2 mM Tris, pH 8.0. ATP-gamma-S and MgCl2 were added at 1 and 2 mM, respectively.
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC (ver. 3.0.2+210831)
最終 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC (ver. 3.0.2+210831)
最終 3次元分類
クラス数: 4 / 平均メンバー数/クラス: 141299 / ソフトウェア - 名称: cryoSPARC (ver. 3.0.2+210831) 詳細: Iterative rounds of 2D classification, 3D classification, and subselection were made. The last round of 3D classification had 4 classes of which 1 was chosen for further refinement and final reconstruction.