Positioned nucleosomes inhibit Dam methylation in vivo.

Escherichia coli Dam DNA methyltransferase can methylate genomic GATC sites when expressed in Saccharomyces cerevisiae. Others have observed changes in the level of methylation at specific sites and suggested that these changes are related to transcriptional state or chromosomal context. To test directly the influence of nucleosome location on the ability of Dam methyltransferase to modify GATC sites in chromatin, we analyzed minichromosomes containing precisely positioned nucleosomes in dam-expressing yeast strains. Levels of methylation at individual GATC sites were rigorously quantified by an oligonucleotide-probing procedure. Within the linker and adjacent 21 bp of nucleosome-associated DNA, GATC sites were highly methylated, whereas methylation was severely inhibited by histone-DNA contacts nearer to the nucleosomal pseudodyad. Other DNA-protein complexes also interfere with Dam methylation. These data are consistent with a model in which nucleosomes exert a repressive influence on the biological functions of DNA by restricting access of trans-acting factors to DNA.