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

Abstract

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.

Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth

“…Heterochromatin components impact H3K27me3 localization in plant and animal cells (58)(59)(60)(61)(62), and Jamieson and Selker observed similar results in Neurospora (63). We therefore performed ChIP-seq to determine if changes in the distribution of H3K27me3 were correlated with sensitivity of DNAdamaging agents in Δdim-5.…”

“…The fact that redistribution of H3K27me3 is deleterious in Neurospora is somewhat surprising; however, a similar observation may have been difficult to make in other experimental systems. In plants and animals, loss of heterochromatin components leads to similar redistribution of H3K27me3 (17,(58)(59)(60)(61)(62), but in these systems, depletion of H3K27me3 from Pc-target regions is sufficient to cause poor growth and developmental defects (74,75). Thus, in many organisms, it would be difficult to determine if the phenotypic defects displayed by H3K9me3-deficient strains were caused by loss of H3K27me3 from native sites or by gain of H3K27me3 in heterochromatin domains.…”

“…H3K9me3, HP1, and 5mC have all been implicated in preventing H3K27me3 redistribution to heterochromatin in animals, and reduction of 5mC leads to redistribution of H3K27me3 in plants (17,(58)(59)(60)(61)(62)71). These observations highlight the need for additional studies to fully elucidate the complex functional and regulatory relationships between heterochromatin and Pc system components.…”

“…Reduction of cytosine methylation in plant and animal cells produced a similar redistribution of H3K27 methylation (59)(60)(61)(62). Positive feedback loops between H3K9 methylation and DNA methylation pathways complicate interpretation of these data, however.…”

“…It has been proposed that redistribution of H3K27me3 to constitutive heterochromatin domains is a compensatory response for maintenance of heterochromatic gene silencing (62,71). To test if this is the case in Neurospora, we asked if Δdim-5; Δset-7 double mutants exhibit increased transcription from constitutive heterochromatin domains.…”