REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells

Abstract

Polycomb Repressive Complex (PRC) 1 and PRC2 regulate genes involved in differentiation and development. However, the mechanism for how PRC1 and PRC2 are recruited to genes in mammalian cells is unclear. Here we present evidence for an interaction between the transcription factor REST, PRC1, and PRC2 and show that RNF2 and REST co-regulate a number of neuronal genes in human teratocarcinoma cells (NT2-D1). Using NT2-D1 cells as a model of neuronal differentiation, we furthermore showed that retinoic-acid stimulation led to displacement of PRC1 at REST binding sites, reduced H3K27Me3, and increased gene expression. Genome-wide analysis of Polycomb binding in Rest−/− and Eed−/− mouse embryonic stem (mES) cells showed that Rest was required for PRC1 recruitment to a subset of Polycomb regulated neuronal genes. Furthermore, we found that PRC1 can be recruited to Rest binding sites independently of CpG islands and the H3K27Me3 mark. Surprisingly, PRC2 was frequently increased around Rest binding sites located in CpG-rich regions in the Rest−/− mES cells, indicating a more complex interplay where Rest also can limit PRC2 recruitment. Therefore, we propose that Rest has context-dependent functions for PRC1- and PRC2- recruitment, which allows this transcription factor to act both as a recruiter of Polycomb as well as a limiting factor for PRC2 recruitment at CpG islands.

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

“…This result is in line with the very recent finding that global inhibition of transcription increases H3K27 methylation in stem cells (41). TFs themselves have been implicated in modulating local levels of H3K27 methylation, and in line with the above model many of these factors serve as transcriptional repressors (e.g., REST and SNAI1) (42)(43)(44). Notably, ES cells lacking REST display only subtle effects on H3K27me3 levels at target loci, whereas more pronounced implications are observed upon neuronal differentiation (42).…”

Principles of nucleation of H3K27 methylation during embryonic development

“…One possible mechanism for PRC1 recruitment to CpG islands is through KDM2B, which binds to unmethylated CpGs via its CxxC zinc finger domain (Farcas et al 2012). Other sequence- based recruitment mechanisms include interactions with sequencespecific TFs such as REST (Dietrich et al 2012;Arnold et al 2013) and RUNX1 (Yu et al 2012).…”

“…7). Although REST is known to associate with Polycomb complexes (Dietrich et al 2012;Arnold et al 2013), this motif is present in only ;1% of H3K27me3 domains. No other TF binding motifs were significantly associated with H3K27me3 domains.…”

Functional Crosstalk Between Lysine Methyltransferases on Histone Substrates: The Case of G9A/GLP and Polycomb Repressive Complex 2

“…Among others, SNAIL, REST, CDYL, and Msx1 (Fig. 5) have been shown to mediate both PRC2 (3,31,49,164) and G9a (34,35,126,163) chromatin targeting, suggesting that common recruiting mechanisms for PRC2 and G9a/GLP might be more common than expected. Given the high affinity of specific TFs for their binding sites and their cellspecific expression, TF-mediated PRC2 G9a/GLP recruitment might be a way to ensure proper PRC2-mediated gene silencing in a cell type-specific manner.…”