Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation

Abstract

Significance Polycomb repressive complex 2 functions in gene repression and acts by methylating histone H3 at lysine 27 (H3K27me3). Despite its relevance, it remains elusive how this complex is recruited to its target sites in the genome. Here, we used repeated genomic targeting in embryonic stem cells to identify DNA sequence determinants that autonomously confer H3K27me3 recruitment. We show that surprisingly small CG-rich DNA sequences are sufficient to recruit H3K27me3, but only if they are devoid of DNA methylation and transcriptional activity. This study provides new insights into the mechanisms recruiting H3K27me3 and the cross-talk between diverse chromatin modifications.

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

“…6G) argues that this is mediated by loss of RNA rather than loss of RNA Pol II transit through chromatin, as originally envisaged. This antagonistic effect of RNA may also contribute to the observed loss of PRC2 binding at CpG islands when positioned next to active promoters and enhancers (Lynch et al 2011;Jermann et al 2014). The results of our in vitro RNA-nucleosome competition assay are consistent with the repression of PRC2 H3K27 methyltransferase activity observed upon addition of RNA in vitro (Cifuentes-Rojas et al 2014;Herzog et al 2014;Kaneko et al 2014b) but suggest this is because RNA competes with nucleosomes for PRC2 binding rather than serving as an allosteric inhibitor of methyltransferase activity.…”

“…Potentially destabilizing association with active genes, the interaction of PRC2 with histone H3 in vitro is inhibited by H3K4me3 (Schmitges et al 2011), and PRC2 methyltransferase activity is repressed by H3K36me2/3 (Schmitges et al 2011;Yuan et al 2011). Consistent with this, the association of PRC2 with CpG islands at active genes is increased upon RNA polymerase (Pol) II inhibition (Riising et al 2014) and correspondingly reduced at CpG islands positioned next to an active promoter (Lynch et al 2011;Jermann et al 2014).…”

“…In ESC, PRC2 and PRC1 are primarily associated with CpG islands at repressed developmental regulator genes (Tanay et al 2007;Ku et al 2008). Insertion of CpG islands or GC-rich sequences into the genome reveals them to be sufficient for PRC2 recruitment (Mendenhall et al 2010;Lynch et al 2011;Jermann et al 2014). PRC2 binding to CpG islands is favored by a lack of DNA methylation (Bartke et al 2010;Lynch et al 2011;Jermann et al 2014), perhaps due to recognition of H2AK119ub deposited by a KDM2B-containing form of PRC1 Cooper et al 2014;Kalb et al 2014).…”

“…Insertion of CpG islands or GC-rich sequences into the genome reveals them to be sufficient for PRC2 recruitment (Mendenhall et al 2010;Lynch et al 2011;Jermann et al 2014). PRC2 binding to CpG islands is favored by a lack of DNA methylation (Bartke et al 2010;Lynch et al 2011;Jermann et al 2014), perhaps due to recognition of H2AK119ub deposited by a KDM2B-containing form of PRC1 Cooper et al 2014;Kalb et al 2014). EED also binds to H3K27me3, generating a positive-feedback loop and suggesting a form of epigenetic memory (Margueron et al 2009).…”

Generalized nucleation and looping model for epigenetic memory of histone modifications

“…Well-known examples are di/trimethylation of histone 3 at lysine 9 (H3K9me2/3) and at lysine 27 (H3K27me2/3), which are enriched in heterochromatin and play a role in gene silencing (3)(4)(5). H3K9me2/3 can spread around centromeres (6) and telomeres (7), and H3K27me2/3 can spread around dedicated response elements within the genome (8,9), causing socalled chromatin position effects by repressing genes within the methylated domains (7,10,11). The enzymes that are responsible for heterochromatic H3K9me2/3 are Clr4 in fission yeast and Suv39h in metazoans, and the PRC2 complex catalyzes H3K27me2/3 (12).…”