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. Combinations of modifications including acetylation, phosphorylation and methylation have been proposed to provide marks recognized by specific proteins. This is exemplified, in both mammalian cells and fission yeast, by transcriptionally silent constitutive pericentric heterochromatin. Such heterochromatin contains histones that are generally hypoacetylated and methylated by Suv39h methyltransferases at lysine 9 of histone H3 (H3-K9). 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. In particular, H3-K9 methylation is thought to provide a marking system for the establishment and maintenance of stably repressed regions and heterochromatin subdomains. 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.

Retracted: Genistein mediated histone acetylation and demethylation activates tumor suppressor genes in prostate cancer cells

“…In contrast, methylation of lysine 9 of H3 is a marker of condensed, inactive chromatin of the sort associated with the inactive X-chromosome and pericentromeric heterochromatin. [48][49][50][51] There is a report that cancer cells have increased overall levels of deacetylation of the known histone target of SIRT1, H4-K16. 52 Moreover, a recent study also suggested that global histone modification in prostate cancer, including acetylation of H3K18 and H4K12, dimethylation of H3K4 and H4R3 and acetylation of H3K9, a target of SIRT1, 53 predict a risk of prostate cancer recurrence.…”

RNAs — Physical and functional modulators of chromatin reader proteins

“…Although this approach is unable to discriminate direct and indirect interactions, these studies revealed that RNA components contribute to targeting of the chromodomain proteins to large heterochromatic domains in mammalian cells. Several groups have shown that heterochromatic localization of HP1α and/or HP1γ is RNase A-sensitive in mouse fibroblasts [22,23]. Consistently, the pericentromeric localization of HP1α was restored upon addition of total or nuclear RNA from the same cellular source to RNase A-treated samples but not upon addition of tRNA or bacterial RNA, suggesting some degree of specificity of the interaction [22].…”

“…Besides the in vitro binding studies, a first cellular link between chromodomain proteins and RNA was established by immunofluorescence-based assays, in which cells were first permeabilized and treated with RNase A before fixation and immunostaining [22]. Although this approach is unable to discriminate direct and indirect interactions, these studies revealed that RNA components contribute to targeting of the chromodomain proteins to large heterochromatic domains in mammalian cells.…”

“…Several recent overview articles have summarized the biology of interactions between RNAs and chromatin modifying enzymes [15,[19][20][21]. However, RNA-binding activities of a subset of 'reader' proteins of chromatin modifications have also been described in different experimental systems [7,13,16,[22][23][24][25]. Here we will summarize the current knowledge on these interactions with particular emphasis on chromodomain proteins, whose RNA-binding activities have been …”

L’hétérochromatine constitutive dans tous ses états

“…Pourtant, la machinerie d'interférence elle-même semble jouer un rôle dans la structuration des centromères puisque l'inactivation de la RNAse III dicer conduit à des altérations de l'architecture hétérochromatinienne centromérique [13]. Par ailleurs, des expériences de traitement de cellules vivantes par la RNase ont montré qu'un composant ribonucléique est nécessaire au maintien de l'organisation des centromères et à la présence de HP1 à l'hétérochro-matine péricentrique [14], mais la nature de l'ARN mis en jeu reste inconnue. Chez le maïs, des ARN d'origine centromérique font partie intégrante du kinétochore [12].…”