Plant Polycomb Repressive Complex 2 and Its Interactors: History
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Subjects: Plant Sciences | Developmental Biology
Contributor:
James Godwin

Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far people are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions.

  • PRC2
  • chromatin
  • protein interactors
  • H3K27me3
  • Arabidopsis
  • transcription
  • development

1. Background

Polycomb Repressive Complex 2 (PRC2) mediates the deposition of the trimethylation of the lysine 27 of the histone 3 (H3K27me3), a histone modification associated with gene repression in eukaryotes [1]. PRC2 was first identified in Drosophila consisting of four core components: Enhancer of zeste (E(z)), a histone methyltransferase unit that catalyses H3K27me3; Extra sex combs (Esc), a WD40 domain protein scaffolding the interactions within the complex; Suppressor of zeste 12 (Su(z)12), a Zinc Finger protein that is essential for binding to nucleosomes; and Nuclear remodeling factor (Nurf55, also called p55), a Trp-Asp (WD) repeat protein involved in nucleosome remodelling [1][2]. After discovering PRC2 complexes in Drosophila as regulators of Hox genes expression, homologs of PRC2 subunits were identified in plants and other organisms [3][4][5]. In Arabidopsis thaliana (Arabidopsis), there are three E(z) homologs—CURLY LEAF (CLF), SWINGER (SWN) and MEDEA (MEA); three Su(z)12 homologs—EMBRYONIC FLOWER 2 (EMF2), VERNALIZATION 2 (VRN2) and FERTILIZATION-INDEPENDENT SEED 2 (FIS2); a single Esc homolog—FERTILIZATION-INDEPENDENT ENDOSPERM (FIE); and there are five Arabidopsis homologs of p55 protein—MULTICOPY SUPPRESSOR OF IRA (MSI) 1–5, but MSI1 is the only one demonstrated to be part of the PRC2 complex [6][7]. Based on their different subunit compositions, at least three PRC2-like complexes controlling different developmental processes have been described in Arabidopsis: the EMF, VRN and FIS complexes [3].
In plants and animals, loss-of-function of core PRC2 subunits results in the abrogation of H3K27me3 levels in PRC2 target genes, which leads to serious developmental defects, highlighting the critical role of PRC2 in development [7][8]. In Arabidopsis chromatin, PRC2 components mimic H3K27me3 localisation [9]. Genome-wide profiling revealed that 20–25% of Arabidopsis genes were marked by H3K27me3, and these genes globally display low expression levels [10][11][12]. Similar percentages of H3K27me3 marked genes were observed in different plant model species (e.g., maize, oilseed rape, rice and Brachypodium distachyon) [13][14][15][16]. These data further demonstrate the importance of PRC2 activity in regulating the expression of key developmental genes in crops and thereby governing the major agricultural traits, e.g., flowering. Besides PRC2’s pivotal function in controlling development, its key role in the regulation of stress responses and other essential cellular processes, such as metabolism, is emerging [17][18][19], although still relatively less understood in both plants and animals. Furthermore, the cells perceive the dynamic environmental signals and translate it into differential chromatin and transcriptional states and this is mediated through histone reader proteins that bind to H3K27me3 and/or that affect local chromatin compaction [18][20]. In a quest to identify protein reader complexes, two plant-specific H3K27me3 readers, namely EARLY BOLTING IN SHORT DAYS (EBS) and its homolog SHORT LIFE (SHL), were recently discovered and were proposed to act within the PcG pathway causing gene repression [21][22]. However, a key question remains unanswered, how do these proteins coordinate their activities with PRC2 to regulate gene expression?
Epigenetic marks such as H3K27me3 can be stably inherited during somatic cell divisions but can be reset during major developmental phase transitions such as the formation of gametes and embryos [23]. In plants, unique mechanisms exist for the inheritance of H3K27me3 marks compared to their animal counterparts. For instance, a recent study in Arabidopsis demonstrated a global reduction in H3K27me3 in the paternal germline (i.e., sperm cells), achieved by the coordinated action of three mechanisms: (1) lack of expression of PRC2 histone methyltransferases encoding units such as CLF, MEA and SWN; (2) active removal by Jumonji-C family methylation erasers (histone demethylases); and (3) the global deposition of a sperm cell specific histone H3 variant, H3.10/HTR10, which is resistant to K27 methylation [24]. Overall, several mechanisms are being elucidated for the transgenerational memory of H3K27me3 in Arabidopsis, but there is much more yet to be discovered.
In animals, the catalytic and non-catalytic function of PRC2 can be regulated by interaction with protein partners [25][26][27]. Similarly, plant PRC2 core components are associated with several other proteins, including PRC1 subunits, transcription factors, chromatin-related proteins, the replication machinery, and proteasomal components leading to the modulation of PRC2 activity and/or resulting in its recruitment to target genes [28]. Essentially, the physical interaction between PRC2 subunits and other proteins helps the researchers to understand the intricate network of protein–protein interactions that occur to regulate PRC2-mediated gene repression during plant developmental transitions and in response to environmental signals. This research highlights the protein interactors of the Arabidopsis PRC2 core subunits identified so far (Figure 1). Nevertheless, VRN2 and its related VRN-PRC2 complex play a highly specialised role in vernalization-induced flowering that has already been extensively reviewed [29][30][31]; hence, the researchers excluded its interactors. The researchers discuss PRC2 recruitment strategies on target genes mediated by the cooperation with accessory proteins and its associated gene repression and explore the impact of PRC2 interactions especially on the modulation of PRC2 activities.
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Figure 1. The physical interaction map of the PRC2 complex in Arabidopsis. Each of the PRC2 core components are represented in different shapes enclosed by a circular box in the centre, E(z) homologs are shown in pink colour—CURLY LEAF (CLF) as a four-pointed star, SWINGER (SWN) as a multi-pointed star and MEDEA (MEA) as a circle; Su(z)12 homologs are shown in golden yellow—EMBRYONIC FLOWER 2 (EMF2) as a rectangle, and FERTILIZATION-INDEPENDENT SEED 2 (FIS2) as a rhombus; the ESC homolog—FERTILIZATION-INDEPENDENT ENDOSPERM (FIE)—is represented as a blue five-pointed star; and the p55 protein homolog—MULTICOPY SUPPRESSOR OF IRA 1 (MSI1)—is represented as a dark green triangle. Physical interactors of PRC2 were functionally grouped into six categories: (I) transcriptional activators and repressors (purple); (II) PRC1 and related factors (light green); (III) DNA replication factors (magenta); (IV) long non-coding RNAs (green thread-like structure); (V) ubiquitin-26S proteasomal components (cyan blue); (VI) other factors (orange); and (VII) histone modifiers (grey). Physical interactors from each category may bind to one or more PRC2 components and the numbers (1–6) within the PRC2 component represent different confirmation techniques used for protein–protein interaction studies: 1—yeast two hybrid; 2—pull down assay; 3—biomolecular fluorescence complementation; 4—fluorescence resonance energy transfer; 5—co-immunoprecipitation; 6—co-immunoprecipitation coupled to mass spectrometry; 7—RNA-immunoprecipitation and binding assays. In the figure, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is placed at the interface between PRC2 and PRC1. Figure created with BioRender.com (accessed on 21 January 2022).

2. PRC2’s Interaction with Ubiquitin-26S Proteasomal Components

In the last decade, there has been emerging evidence of the regulation of PRC2 components by their interaction with members of the ubiquitin-26S proteasome, especially with E3 ubiquitin ligases, which facilitate the transfer of ubiquitin to a substrate [32][33][34]. The ubiquitination of proteins may cause subsequent protein degradation [35], but can also promote changes in the function or activity of the ubiquitinated proteins including chromatin-associated proteins [36]. The ubiquitination of core PRC2 subunits for the control of PRC2 activity and the subsequent protein turnover of PRC2 components will be discussed here.
UPWARD CURLY LEAF1 (UCL1), a plant-specific F-box component of the well-characterised Skp, Cullin, F-box (SCF)-containing E3 ligase complex, physically associates with CLF in the nucleus and subsequently ubiquitinates CLF to target it for degradation via the ubiquitin-26S proteasome pathway. This interaction seems to be quite specific as UCL1 does not interact with MEA [37]. Overexpression of UCL1 reduces CLF protein levels and alters the expression levels of CLF target genes, suggesting a negative regulation of CLF by UCL1 [37]. Moreover, the phenotypes of mutants affected in UCL1 and CLF indicate that they may act in the same genetic pathway in which UCL1 may be a negative regulator of CLF [37].
Another multimeric E3 ubiquitin ligase complex contains CULLIN 4 (CUL4), a scaffolding protein, and DAMAGED DNA-BINDING PROTEIN 1 (DDB1), an adaptor protein that associates with the substrate protein and targets it for degradation [38]. In Arabidopsis, DDB1 physically interacts with MSI1 and CUL4, indicating the possibility for a CUL4–DDB1–MSI1 protein complex [39]. The question was asked as to whether MSI1 could act as a substrate receptor of this E3 ligase complex. The results from two independent studies revealed that MSI1 protein turnover is indeed not under the control of CUL4 [39][40]. However, when CUL4’s function was compromised, silencing of paternal MEA was released in the seeds due to the reduction in H3K27me3 levels at this locus and overall [39], pointing to a mediation of CUL4–DDB1 in the activity of the FIS–PRC2 complex. In the cul4 mutant, there was significant decrease in H3K27me3 levels on FLC and its downstream target FT [40], further supporting CUL4-DDB1 function in the regulation of PRC2 activities.
CUL4 and DDB1 physically interact with another p55 ortholog, MSI4, and form the CUL4–DDB1–MSI4 complex. MSI4 also interacted with CLF, but not FIE, in Y2H and in planta BiFC assays [40]. Furthermore, loss-of-function mutations of MSI4 reduce H3K27me3 on FLC and FT, resulting in their upregulation and causing a late-flowering phenotype. Therefore, direct regulation of CLF–PRC2 activity by the CUL4–DDB1–MSI4 E3 ubiquitin ligase was plausible [40]. Recently, a plant-specific protein, EMBRYO DEFECTIVE 1579 (EMB1579), implicated in embryo development [41], was demonstrated to recruit and phase condensate CUL4–DDB1–MSI4 [42]. In addition, EMB1579 facilitates the physical association of the CUL4–DDB1–MSI4 complex with CLF and contributes to maintaining the proper H3K27me3 levels on FLC, subsequently controlling flowering [42]. In animals, studies are emerging on how ubiquitination modulates liquid–liquid phase separation of PRCs to mediate large-scale chromatin compaction [43], whereas in plants, there is increasing evidence of the conservation and importance of liquid–liquid phase separation in the organisation of the nuclear space [44]. Understanding the interface among ubiquitination, liquid–liquid phase separation and PRC2 may provide key mechanistic insights into PRC2’s recruitment and dynamics.

3. PRC2’s Interaction with DNA Replication Components

During cell division, PRC2’s interaction with DNA-replication-related proteins enables the transmission of H3K27me3 to the daughter cells. Understanding PRC2-mediated gene silencing in a replication-coupled manner through its interaction with members of the replication machinery is crucial to dissect the molecular mechanisms behind the inheritance of the H3K27me3 mark on canonical and histone variants in post-replicative chromatin. Thus, in this section, the researchers will highlight the physical association of PRC2 with components of the DNA replication machinery (Figure 1).

3.1. FASCIATA 1

CHROMATIN ASSEMBLY FACTOR 1 (CAF-1) is an evolutionarily conserved heterotrimeric chaperone complex that facilitates the association and deposition of histone tetramers (H3 and H4) onto nascent chromatin [45][46]. In Arabidopsis, three subunits, namely FASCIATA1 (FAS1), FAS2 and MSI1, form the functional CAF1 complex in vitro [47]. The analyses of mutants affected in CAF-1 subunits revealed its essential role in controlling pollen development and apical meristem architecture [48][49]. FAS1’s direct interaction with CLF, LHP1 and AtRING1A was confirmed by in vitro pull-down and co-IP assays [49]. Strikingly, FAS1 colocalises with PRC2 and PRC1 components, within the DNA replication foci, suggesting that both PRC2–CAF1 and PRC1–CAF1 interactions occur at the DNA replication sites [49], to further illustrate the possible interplay between both PRCs. In addition, CAF1 deposits the histone variant H3.1 at the replication fork and facilitates the maintenance of H3K27me3 in the new synthesised DNA molecule [49].

3.2. ENHANCER OF LHP1 (EOL1)

ENHANCER OF LHP1 (EOL1) is a plant homolog of yeast Chromosome transmission fidelity 4 (Ctf4), which acts in the DNA helicase complex during DNA replication [50]. EOL1 is a nuclear protein produced in dividing cells and is associated with the replication machinery in Arabidopsis [51]. EOL1 physically interacts with SWN, CLF and LHP1. The eol1 mutant acts as an enhancer of the clf mutant and eol1;clf plants have smaller rosette leaves and flower earlier than clf plants. H3K27me3 levels at FT, AG and SEP3 were increased in eol1;clf but remained unchanged in the eol1 single mutant. In addition, some H3K27me3-enriched genes showed increased expression in eol1;lhp1 compared to lhp1 mutants since the loss of function of EOL1 further increases the misexpression of H3K27me3 target genes that are already upregulated in the lhp1 mutant. Overall, this research proposed that EOL1 function is required for LHP1-PRC2 to maintain H3K27me3 levels at target genes in dividing cells [51], as EOL1 is exclusively expressed in actively dividing cells and is required for the inheritance of H3K27me3 marks during replication.

3.3. DNA Polymerases

In Arabidopsis, EARLY IN SHORT DAYS 7 (ESD7) (also called POL2a/ABA OVERLY SENSITIVE 4 (ABO4)) encodes the catalytic subunit of the DNA Polymerase epsilon (Pol ε), which is involved in the synthesis of the leading DNA strand during replication and has been found to be essential for the viability of the embryo [52][53]. ESD7 physically interacts with CLF, EMF2 and MSI1. CLF and EMF2 are recruited to FT and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) chromatin by ESD7 to maintain the H3K27me3 levels on these loci [54]. Mutants of other DNA polymerases subunit-encoding genes, such as Pol-α INCURVATA2 (ICU2) and Pol-δ POLD2, impact H3K27me3 distribution in several genes and enhance the abnormal phenotype of PcG mutants [55]; however, a direct interaction of these DNA polymerases with PRC2 subunits still needs to be demonstrated. Despite these promising links, the role of DNA polymerases in nucleosome reconstitution and the way in which the deposition of post-translational histone modifications is coupled to the activity of these enzymes remain elusive.

4. PRC2’s Interaction with Histone Modifiers

The functional implications of histone modifications for the recruitment of PRC2, or in the regulation of its activities, is not well understood. Importantly, co-occurring of histone modification appears to influence PRC2 activity and there is an intricated orchestration of PRC2 binding to other histone-modifying enzymes. In this section, we will explore the interaction of PRC2 with histone modifiers (Figure 1).

4.1. INCURVATA 11 (ICU11)

In Arabidopsis, INCURVATA 11 (ICU11) encodes a 2-oxoglutarate-dependent dioxygenase (2OGD). The 2OGD domain of ICU11 belongs to the same enzymatic superfamily as Jumonji C-domain histone demethylases [56]. The icu11 mutant shows a slight increase in H3K36me3 levels, an active histone mark, suggesting a role of ICU11 in H3K36me3 demethylation [56]. The icu11 mutant shares many pleotropic phenotypes with the emf1 and emf2 mutants (e.g., small-sized cotyledon, leaf curling and early flowering) and ICU11 copurifies with CLF, SWN, FIE, MSI1 and EMF2 and other PRC2 accessory components such as EMF1, LHP1 and TRB1–3 [56]. The physical cooperation between histone methyltransferases and demethylases has been proposed to contribute to positive feedback loops for the transition between opposite chromatin stages (e.g., from open to closed chromatin conformation) and modelling studies in Schizosaccharomyces pombe predict that this kind of physical coupling facilitates the bi-stability of opposing chromatin states [57][58]. In Arabidopsis, another example that validates this hypothesis is the interaction of the H3K27me3 demethylase EARLY FLOWERING 6 (ELF6) with the H3K36me3 methyltransferase SET DOMAIN GROUP 8 (SDG8). In this case, the ELF6-SDG8 interaction switches chromatin from a closed to an open stage [59].

4.2. ARABIDOPSIS HOMOLOG OF TRITHORAX 1 (ATX1)

ARABIDOPSIS HOMOLOG OF TRITHORAX 1 (ATX1) catalyses the deposition of H3K4me3 and belongs to the Trithorax Group (TrxG) pathway, which plays an antagonistic role in PRC2 proteins by means of gene activation [60]. ATX1 and CLF physically bind to each other in Y2H and BiFC assays despite their, in principle, antagonistic activities. Loss-of-function mutations in ATX1 or CLF genes result in the repression or activation of the floral homeotic gene AG, respectively [61]. Interestingly, a lack of both ATX1 and CLF functions results in partial restoration of H3K4me3 and H3K27me3 on the AG nucleosomes. On the other hand, restoring AG repression rescues the respective single-mutant phenotype (atx1 and clf). Therefore, it is suggested that ATX1 and CLF-coordinated activities generate the bivalent marks H3K4me3 and H3K27me3 at the AG locus [61]. Besides the AG locus, these types of bivalent chromatin marks, mediated by TrxG and PcG, were reported at other loci such as FLC, SUP and APETALA 1 (AP1) [17][61]. In animals, the presence of H3K4me3 and H3K27me3 marks at silent embryonic stem cell loci has been proposed to act as an inducer of a bivalent transcriptional state that reduces noise and that poses genes for transcription later in development [62]. However, more recent models have been suggested in yeast in which the antagonistic TrxG/PcG interplay is required for the bistable regulation of target genes [58].

4.3. HISTONE DEACETYLASES (HDAC)

HISTONE DEACETYLASES (HDACs) catalyse the deacetylation of lysine residues in histones and regulate gene expression [63]. To date, a few HDACs from plants have been characterised. In Arabidopsis, the most studied HDACs, HISTONE DEACETYLASE 6 (HDA6), HDA9 and HDA19, are involved in the regulation of developmental processes and environmental responses [64][65][66]. It is shown that HDA19 co-purifies with MSI1 to fine-tune ABA signalling by binding to ABA receptor genes [67]. Recently, HDA9, a homolog of HDA19, was shown to preferentially deacetylate H3K27 to pave PRC2-mediated H3K27me3 deposition at various loci, resulting in transcriptional repression. These findings also suggest that H3K27 deacetylation may be a prerequisite for H3K27me3 activity and gene repression [68][69]. Furthermore, it was demonstrated that HDA9 and HDA19 are required for PRC2 enrichment on FLC chromatin [69]. Another report showed that HDA9 and HDA19 physically associate with VAL1 and VAL2, and VAL2 was also reported to bind HDA6 [70][71], suggesting that some HDACs are interlinked with PRC2 through VAL proteins. Overall, it seems that there is a concerted action between at least certain HDACs and PRC2 for the repression of specific target genes in Arabidopsis, whether this is conserved throughout the HDAC family and in other plant species is still an unresolved question.

5. Conclusions and Perspectives

More recently, genome-wide enrichment of H3K27me3 in important crops, such as rice, maize, barley and oilseed rape, has been made available [14][16][72], demonstrating a similar epigenomic landscape but also special features in the deposition of this mark. Phylogenetic analyses also demonstrate a good conservation of the proteins of the complex and the possible existence of similar PRC2 subcomplexes [4][73]. However, much more research is needed to understand how PRC2’s functions are regulated in these species through the conservation of its protein network or through the formation of novel species-specific interactions. It's proposed that a better understanding of PRC2 interactors in species of agronomic interest is capital to the discovery of new molecular tools for a tighter control of plant development and responses and for the breeding of new crop varieties with enhanced traits to better adapt their development to the environment.

This entry is adapted from the peer-reviewed paper 10.3390/epigenomes6010008

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