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TitleNucleosome spacing regulates linker methylation by DNMT3A2/3B3.
Journal, issue, pagesMol Cell, Vol. 86, Issue 5, Page 834-850.e9, Year 2026
Publish dateMar 5, 2026
AuthorsXiaoyan Xie / Minmin Liu / Gabriella N L Chua / X Edward Zhou / Michelle L Dykstra / Shixin Liu / Peter A Jones / Evan J Worden /
PubMed AbstractDe novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get ...De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get targeted by DNMT3 enzymes are not understood. We show that nucleosome spacing controls linker DNA methylation and H3K36me2 recognition by human DNMT3A2/3B3, linking de novo methylation to chromatin architecture. We present structures of DNMT3A2/3B3 bound to dinucleosomes, revealing that short linkers promote dinucleosome bridging, blocking access to linker DNA and suppressing methylation, whereas long linkers allow DNMT3A2/3B3 to engage each nucleosome separately and methylate linker DNA. Finally, we show that DNMT3A2/3B3 positions proline-tryptophan-tryptophan-proline (PWWP) domains to scan for H3K36me2. However, H3K36me2 recognition is blocked when DNMT3A2/3B3 bridges dinucleosomes with short linkers, imposing an additional structural constraint on DNMT3A2/3B3 function. Together, these findings uncover the mechanisms that govern de novo methylation in chromatin and explain how DNMT3 enzymes target linkers in cells.
External linksMol Cell / PubMed:41742418 / PubMed Central
MethodsEM (single particle)
Resolution3.51 - 5.51 Å
Structure data

EMDB-71604: Consensus map for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight-base-pair linker
Method: EM (single particle) / Resolution: 3.84 Å

EMDB-71606: Focus map of DNMT3A2/3B3 tetramer2 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker
Method: EM (single particle) / Resolution: 5.51 Å

EMDB-71607: Focus map of nucleosome 1 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker
Method: EM (single particle) / Resolution: 4.99 Å

EMDB-71608: Focus map of nucleosome 2 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker
Method: EM (single particle) / Resolution: 3.51 Å

EMDB-71609: Focus map of nucleosome1_PWWP1 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker
Method: EM (single particle) / Resolution: 4.99 Å

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  • Homo sapiens (human)

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