Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation.

Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1LSH/HELLS), 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 MET1Dnmt1, 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. [Display omitted] • DDM1 remodeling promotes H3.1 H2A.W deposition and DNA methylation • Cryo-EM structure reveals contacts with variant H3 residues and deacetylated H4 tails • An autoinhibitory N terminus and helicase S–S bond regulate DDM1 activity • Male germline H3.3 placeholder variant contributes to epigenetic inheritance How DDM1 drives DNA methylation and epigenetic inheritance is unknown. Through high-resolution genomic and structural analyses, it is shown how DDM1 is recruited to nucleosomes and provides MET1 access to naked replicated DNA, ensuring epigenetic inheritance of DNA methylation. [ABSTRACT FROM AUTHOR]