CDCA7 facilitates MET1 mediated CG methylation maintenance at pericentromeric and centromeric chromatin [BiSulfite-seq]
DNA methylation is a conserved epigenetic modification critical for transposable element (TE) silencing and genome stability. However, how methyltransferases maintain CG methylation within compact heterochromatin remains unclear. In humans, CDCA7 is required for DNA methylation inheritance at juxta-centromeres, and mutations impairing its binding to heterochromatic nucleosomes lead to satellite DNA hypomethylation and ICF syndrome. In Arabidopsis thaliana, we identified two CDCA7 orthologs, CDCA7A and CDCA7B, as key regulators of DNA methylation. Loss of both causes CG hypomethylation specifically at pericentromeric and centromeric regions. Machine learning analysis revealed that nucleosome density, H1 enrichment, the H2A.W variant, and H3K9me2 levels predict methylation loss in cdca7a cdca7b mutants. Notably, H1 depletion restores methylation in these mutants, indicating that CDCA7A and CDCA7B enable MET1 access to H1-containing nucleosomes and are particularly required for methylation maintenance in compact chromatin. Additionally, in h1.1 h1.2 mutants, CG methylation increases modestly at pericentromeric regions but significantly at centromeric sites, revealing an inhibitory role for H1 in centromeric methylation. This hypermethylation is abolished in h1.1 h1.2 cdca7a cdca7b quadruple mutants, demonstrating that CDCA7A and CDCA7B promote MET1 activity at heterochromatic nucleosomes independently of H1. Together, these results establish CDCA7A and CDCA7B as conserved and versatile chromatin remodelers that facilitate MET1 activity within heterochromatin. Overall design: Employ WGBS and RNA-seq to study the role of CDCA7 in DNA methylation maintenance