Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component

Abstract

Post-translational modification of histone tails is thought to modulate higher-order chromatin structure^1,2,3. Combinations of modifications including acetylation, phosphorylation and methylation have been proposed to provide marks recognized by specific proteins⁴. This is exemplified, in both mammalian cells and fission yeast, by transcriptionally silent constitutive pericentric heterochromatin. Such heterochromatin contains histones that are generally hypoacetylated⁵ and methylated by Suv39h methyltransferases at lysine 9 of histone H3 (H3-K9)^6,7. Each of these modification states has been implicated in the maintenance of HP1 protein–binding at pericentric heterochromatin, in transcriptional silencing and in centromere function^{7,8,9,10,11,12}. In particular, H3-K9 methylation is thought to provide a marking system for the establishment and maintenance of stably repressed regions and heterochromatin subdomains^3,13. To address the question of how these two types of modifications, as well as other unidentified parameters, function to maintain pericentric heterochromatin, we used a combination of histone deacetylase inhibitors, RNAse treatments and an antibody raised against methylated branched H3-K9 peptides. Our results show that both H3-K9 acetylation and methylation can occur on independent sets of H3 molecules in pericentric heterochromatin. In addition, we identify an RNA- and histone modification–dependent structure that brings methylated H3-K9 tails together in a specific configuration required for the accumulation of HP1 proteins in these domains.