REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells

Nikolaj Dietrich,Mads Lerdrup,Erik Södersten,Niels Tommerup,Shuchi Agrawal-Singh,Mads Bak,Eskild Landt,Juri Rappsilber,Klaus Hansen,Hiten D Madhani

doi:10.1371/journal.pgen.1002494

Nikolaj Dietrich, Mads Lerdrup + Show 8 more

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https://doi.org/10.1371/journal.pgen.1002494

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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.

Highlights

Polycomb group (PcG) proteins are epigenetic regulators of gene expression and play an essential role during embryonic development [1]
In line with REST being a repressor of neuronal genes, we found that PRC1 and Polycomb repressive complex 2 (PRC2) co-localized with REST at genes involved in neuronal development and got displaced during neuronal differentiation
We were interested to examine whether the transcription factor REST and the PRC1 complex would interact in vivo, encouraged by previous observations, where we identified REST in a doubletag purification of the CBX8 interacting protein, HAN11 (WDR68) (Figure S1; see the information in Procedure S1)

Summary

Introduction

Polycomb group (PcG) proteins are epigenetic regulators of gene expression and play an essential role during embryonic development [1]. The Polycomb repressive complex 2 (PRC2) is the only known enzyme that mediates di- and tri-methylation of histone H3 on lysine 27 (H3K27Me2/3), modifications believed to be required for PcG-mediated gene repression [2,3,4,5]. H3K27Me3 can function as an epigenetic mark for the recruitment of PRC1, a large heterogenous complex [9], which among others include the Cbx- and Rnf (Ring1B) proteins. Rnf catalyzes the ubiquitination of histone H2A on lysine 119 (H2AK119Ubi) [10,11] and as for the members of the PRC2 complex, disruption of the Rnf gene in mouse causes a similar developmental phenotype with arrest at gastrulation [12]. Rnf has recently been shown to be part of at least two additional gene regulatory complexes, the E2F6.com-1 complex [13] and the Fbxl10-BcoR complex [14]

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