UCSF

Specifying cellular identity requires silencing cell-type inappropriate genes. In eukaryotes, this is accomplished by varying the packaging density of nucleosomes, segmenting chromosomes into regions of tight (heterochromatin) and loose (euchromatin) packing. Packaging is directed in part by dimethylation of Histone 3 lysine 9 (H3K9me2). H3K9me2 is catalyzed by the G9a-GLP heterodimer, which, like other heterochromatic lysine methyltransferases, possess product-recognition, or 'reading' domains. We first explore how reading by G9a-GLP affects nucleosome methylation in vitro. We unveil that a cis composition of heterotypic product-recognition domains functions to regulate nucleosome dimethylation but not monomethylation. Our findings illuminate the pivotal role of methyl nucleosome binding by these domains in facilitating dimethylation. We then turn our attention to the cell, where H3K9me2 is enriched at the nuclear periphery. We find that knocking out putative H3K9me2 readers, which releases the mark from the nuclear periphery, affects the genomic abundance and distribution of H3K9me2 specifically during differentiation. These insights underscore the complexity of the methylation landscape and open doors to understanding the interplay of molecular recognition and enzymatic activity in chromatin modification and ultimately, cell identity.