Dynamic Competition of Polycomb and Trithorax in Transcriptional Programming

Abstract

Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type-specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type-specific transcriptional programming with exquisite fidelity is essential for normal development.

Keywords: Polycomb; Trithorax; bivalent chromatin; epigenetics; gene regulation.

Figure 1

PcG complexes in Drosophila and mammals. PcG proteins are classified into two major complexes: (a) PRC1 and (b) PRC2. Homologous core complex subunits are color coded between Drosophila (left, brown) and mammals (right, blue), and their common catalytic subunits are indicated [dRing or RING1A/B in all PRC1 complexes and E(z) or EZH1/2 in PRC2]. The core complexes are diversified by interactions with accessory proteins, especially in mammals. Accessory subunits can be mutually exclusive as in mammalian PRC2.1 and PRC2.2. Similarly, mammalian PRC1 is divided into cPRC1 (canonical PRC1) and vPRC1 or ncPRC1 (variant or noncanonical PRC1), as initially defined by Gao et al. (38). Analogous in-depth studies of Drosophila vPRC1/ncPRC1 have not been reported. Protein–protein contacts presented here are not meant to be accurate. In many cases, they are not known in detail, although substantial progress has occurred recently (–60, 81). Likewise, depicted complexes are meant to represent a general view, but the existence of additional configurations or cell type– and tissue type–divergent versions is also likely. Abbreviations: PcG, Polycomb Group; PRC1 and PRC2, Polycomb Repressive Complexes.

Figure 2

Assembly of PcG complexes at target loci. (a) Drosophila PREs bind many different DNA binding proteins including Pho/Phol, Spps, GAF, and Cg (63), and a combination of these PRE binding proteins is typically required for recruitment of PRC1 and PRC2. Genome-wide ChIP studies have shown that, although Pc (a component of PRC1) can spread beyond the recruitment sites via binding to H3K27me3, the highest concentration is near PREs. The genomic binding pattern of H2AK118ub is less well defined in flies (26). (b) In mammals, PcG complexes are enriched at unmethylated CGIs. KDM2B of vPRC1.1 and SUZ12, JARID2, and MTF2 of PRC2 all have affinity for GC-rich DNA sequences that may help drive assembly at nucleation sites. vPRC1 ubiquitinylates H2AK119 in mammals, which facilitates recruitment of PRC2 via JARID2. Further, EED of PRC2 and CBX of cPRC1 bind H3K27me3 to drive self-propagation or spreading of the repressive mark. Abbreviations: CGI, CpG island; ChIP, chromatin immunoprecipitation; cPRC1, canonical PRC1; Pc, Polycomb; PcG, Polycomb Group; PRC1 and PRC2, Polycomb Repressive Complexes; PRE, Polycomb response element; vPRC1, variant PRC1.

Figure 3

Model for Polycomb Group (PcG) domain establishment. (❶) PcG domain boundaries are defined in Drosophila by either actively transcribed genes or insulator proteins and in mammals by CTCF proteins, and these boundaries may form similarly in flies and in mammals (3). (❷) In both organisms, PcG proteins appear to first engage with recruitment sites (red lines) within PcG target domains. (❸) The recruitment sites can be either strong or weak and either cell type–, tissue type–, or developmental stage–specific. After the initial recruitment, two parallel events happen: (❹) PcG complexes modify flanking histone tails (modified histones are shown with blue spheres) and interactions between the PcG proteins bound to the recruitment sites drive changes in 3D structure of the domain. The initial histone modifications and changes in 3D architecture of the domain drive further recruitment of PcG complexes and cause modification of the rest of the histones to establish the PcG domain. (➎) Finally, the PcG domains form phase-separated droplets either individually or by fusing with each other. These phase-separated droplets are also known as PcG bodies.

Figure 4

Bivalent chromatin marks and their resolution upon differentiation. (a) Mammalian embryonic stem cells are derived from the inner cell mass of blastocysts. Embryonic stem cells not only are capable of self-renewal but also are pluripotent, meaning they can give rise to many cell types in the body. (b) Many developmental genes in pluripotent cells are marked with bivalent chromatin in which both active H3K4me3 and silent H3K27me3 modifications coexist. This bivalency typically is resolved into either active or silent states during differentiation.

Figure 5

The bivalent master switch model. During embryonic development in Drosophila, PRC1 and specific coactivator proteins are proposed to form bivalent protein complexes on transcriptionally poised genes. The coactivator module includes a histone acetyltransferase that can both catalyze and recognize acetylation marks, whereas a separate subunit can bind the H3K4me3 chromatin mark at active or bivalent promoters. In contrast, PRC1/PRC2 enrichment is reinforced by the H3K27me3 silencing mark and unacetylated nucleosomes. The choice between a transcriptionally active or silent state may be triggered by combinations of specific transcription factors that alter the acetylation state of the local chromatin environment, favoring increased association of coactivators or PRC2, respectively. If some level of co-occupancy is maintained, the resulting transcriptional states may be reversible (dotted lines) by changes in critical thresholds of competing transcription factors during subsequent differentiation. Although this model rests largely on protein interactions observed in Drosophila, it is compatible with the responsive model for PcG targeting in mammalian cells (95). In an extension of that model, mammalian PcG and TrxG proteins may compete for interaction at CpG islands and be influenced by local acetylation, without necessarily interacting physically as observed in Drosophila embryos. Abbreviations: PcG, Polycomb Group; PRC1 and PRC2, Polycomb Repressive Complexes; TrxG, Trithorax Group.