DDM1/Lsh remodelers allow methylation of DNA wrapped in nucleosomes

Eukaryotic DNA is wrapped around histone octamers to form nucleosomes, which are separated by linker DNA bound by histone H1. In many species, the DNA exhibits methylation of CG dinucleotides, which is epigenetically inherited via a semiconservative mechanism. How methyltransferases access DNA within nucleosomes remains mysterious. Here we show that methylation of nucleosomes requires DDM1/Lsh nucleosome remodelers in Arabidopsis thaliana and mouse. We also show that removal of histone H1, which partially restores methylation in ddm1 mutants, does so primarily in the linker DNA between nucleosomes. In h1ddm1 compound mutants, substantial portions of the genome exhibit dramatically periodic methylation that approaches wild-type levels in linker DNA but is virtually absent in nucleosomes. We also present evidence that de novo methylation supplements semiconservative maintenance of CG methylation across generations. Overall, our results demonstrate that nucleosomes and H1 are barriers to DNA methylation, which are overcome by DDM1/Lsh nucleosome remodelers. Bisulfite sequencing to determine single-base DNA methylation: 4 different genotypes from F4 generation, without replicates; MNase sequencing to identify nucleosome positions genomewide: single generation in leaf tissue for 4 different genotypes, 2 or 3 biological replicates; RNA-seq to define expression deciles in wild-type: single generation in leaf tissue for WT, 2 replicates.