Redundant Mechanisms to Form Silent Chromatin at Pericentromeric Regions Rely on BEND3 and DNA Methylation

Constitutive heterochromatin is typically defined by high levels of DNA methylation and H3 lysine 9 trimethylation (H3K9Me3), whereas facultative heterochromatin displays DNA hypomethylation and high H3 lysine 27 trimethylation (H3K27Me3). The two chromatin types generally do not coexist at the same loci, suggesting mutual exclusivity. During development or in cancer, pericentromeric regions can adopt either epigenetic state, but the switching mechanism is unknown. We used a quantitative locus purification method to characterize changes in pericentromeric chromatin-associated proteins in mouse embryonic stem cells deficient for either the methyltransferases required for DNA methylation or H3K9Me3. DNA methylation controls heterochromatin architecture and inhibits Polycomb recruitment. BEND3, a protein enriched on pericentromeric chromatin in the absence of DNA methylation or H3K9Me3, allows Polycomb recruitment and H3K27Me3, resulting in a redundant pathway to generate repressive chromatin. This suggests that BEND3 is a key factor in mediating a switch from constitutive to facultative heterochromatin. [Display omitted] •PICh reveals pericentromeric heterochromatin-associated proteins in ESCs•H3K9me3 controls maintenance DNA methylation and the chromosomal passenger complex•DNA methylation controls pericentromeric architecture and Polycomb binding•BEND3 mediates Polycomb recruitment in the absence of H3K9Me3 or DNA methylation Saksouk et al. use a quantitative version of the Proteomics of Isolated Chromatin segment method to establish pericentromeric heterochromatin composition and analyze how H3K9me3 and DNA methylation regulate this locus in embryonic stem cells. A model in which methylation-sensitive DNA binding proteins control the switching of the locus into distinct epigenetic states is proposed.