The interplay of histone modifications – writers that read
2015; Springer Nature; Volume: 16; Issue: 11 Linguagem: Inglês
10.15252/embr.201540945
ISSN1469-3178
AutoresTianyi Zhang, Sarah Cooper, Neil Brockdorff,
Tópico(s)RNA modifications and cancer
ResumoReview16 October 2015Open Access The interplay of histone modifications – writers that read Tianyi Zhang Tianyi Zhang Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK Search for more papers by this author Sarah Cooper Corresponding Author Sarah Cooper Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK Search for more papers by this author Neil Brockdorff Neil Brockdorff Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK Search for more papers by this author Tianyi Zhang Tianyi Zhang Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK Search for more papers by this author Sarah Cooper Corresponding Author Sarah Cooper Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK Search for more papers by this author Neil Brockdorff Neil Brockdorff Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK Search for more papers by this author Author Information Tianyi Zhang1,‡, Sarah Cooper 1,‡ and Neil Brockdorff1 1Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK ‡These authors contributed equally to this work *Corresponding author. Tel: +44 1865 613230; E-mail: [email protected] EMBO Reports (2015)16:1467-1481https://doi.org/10.15252/embr.201540945 See the Glossary for abbreviations used in this article. PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract Histones are subject to a vast array of posttranslational modifications including acetylation, methylation, phosphorylation, and ubiquitylation. The writers of these modifications play important roles in normal development and their mutation or misregulation is linked with both genetic disorders and various cancers. Readers of these marks contain protein domains that allow their recruitment to chromatin. Interestingly, writers often contain domains which can read chromatin marks, allowing the reinforcement of modifications through a positive feedback loop or inhibition of their activity by other modifications. We discuss how such positive reinforcement can result in chromatin states that are robust and can be epigenetically maintained through cell division. We describe the implications of these regulatory systems in relation to modifications including H3K4me3, H3K79me3, and H3K36me3 that are associated with active genes and H3K27me3 and H3K9me3 that have been linked to transcriptional repression. We also review the crosstalk between active and repressive modifications, illustrated by the interplay between the Polycomb and Trithorax histone-modifying proteins, and discuss how this may be important in defining gene expression states during development. Glossary AEPB2 AE-binding protein 2 ASH2L absent, small, or homeotic-like ATRX5/6 Arabidopsis Trithorax-related protein 5/6 BEND3 Ben domain containing 3 BLOCS broad local enrichments BRE1 Brefeldin-A sensitivity protein 1 CBX chromobox CDYL chromodomain protein, Y-like CFP1 CXXC finger protein 1 ChIP-sequencing chromatin immunoprecipitation followed by DNA sequencing CpG cytosine-phosphate-guanine CTCF CCCTC-binding factor CTBP2 C-terminal-binding protein 2 CTD C-terminal domain DNMT3A/B DNA methyltransferase 3A/B DOT1 disruptor of telomeric silencing 1 DOT1L DOT1-like DPY30 dumpy-30 protein homolog EAF3 Esa1p-associated factor 3 EED embryonic ectoderm development ESC embryonic stem cell EZH2/1 enhancer of zeste homolog 2/1 FRAP fluorescence recovery after photobleaching G9a/GLP G9a and G9a-like protein H2AK119u1 histone H2A lysine 119 monoubiqutination H2BK120u1 histone H2B lysine 120 monoubiqutination H2BK34u1 histone H2B lysine 34 monoubiqutination H3K27me1/2/3 histone H3 lysine 27 mono/di/trimethylation H3K36me1/2/3 histone H3 lysine 36 mono/di/trimethylation H3K4me1/2/3 histone H3 lysine 4 mono/di/trimethylation H3K9me1/2/3 histone H3 lysine 9 mono/di/trimethylation HAT histone acetyltransferase HBO1 histone acetyltransferase bound to ORC 1 HDAC histone deactylase complex HMT histone methyltransferase Hox gene homeobox-containing gene HP1 heterochromatin protein 1 JARID2 jumonji, AT-rich interactive domain 2 KDM2A/B lysine demethylase protein 2A/B MBD methyl binding domain MES-4 mesoderm expressed 4 MLL1/2/3/4 mixed-lineage leukemia 1/2/3/4 complex MSL1/2 male-specific lethal 1/2 NO66 nucleolar protein 66 NSD1/2/3 nuclear receptor-binding SET domain protein 1/2/3 NuA3/4 nucleosomal acetyltransferase of histone H3/H4 NURD nucleosome remodeling and deacetylase P300/CBP P300- and CREB-binding protein PAF polymerase-associated factor PCGF1/2/3/4/5/6 Polycomb group ring finger 1/2/3/4/5/6 PCL1/2/3 Polycomb-like 1/2/3 PH polyhomeotic PHD finger plant homeodomain finger Pol II RNA polymerase II PRC1 Polycomb repressive complex 1 PRC2 Polycomb repressive complex 2 RAD6 ras-related associated with diabetes protein 6 RBBP5 retinoblastoma-binding protein 5 RING1A/B really interesting new gene 1A/B RNF20/40 ring finger protein 20/40 RpAb46/48 Rb-associated protein 46/48 RPD3S reduced potassium dependency 3S complex RYBP RING1- and YY1-binding protein SAGA Spt-Ada-Gcn5 acetyltransferase SET domain Su(var)3-9, enhancer-of-zeste and Trithorax domain SETD1A/B SET domain containing 1A/B SETD2 SET domain containing 2 SETMAR SET domain and mariner transposase fusion containing protein 2 SMYD2 SET and MYND domain-containing protein 2 SUV3-9 H1/H2 suppressor of variegation 3-9 homolog 1/2 SUZ12 Suppressor of zeste 12 homolog TrxG Trithorax group TSS transcription start site WDR5 WD repeat-containing protein 5 YAF2 YY1-associated factor 2 ZMYND11 zinc finger, MYND-type containing 11 Introduction In eukaryotes, DNA is packaged in the form of chromatin. The basic unit of chromatin, the nucleosome, is comprised of 147 bp of DNA wrapped around a histone octamer made of two dimers of H2A and H2B and a tetramer of H3 and H4 proteins. The N- and C-terminal histone tails protrude from the nucleosome core and have the potential to interact with adjacent nucleosomes and the linker DNA. All histones can be posttranslationally modified, and the sites of modification are often on the histone tails. These modifications can regulate chromatin structure directly and frequently act as binding sites for the recruitment of other non-histone proteins to chromatin. The most abundant histone modifications are acetylation, phosphorylation, methylation, and ubiquitylation, although many other modifications have been reported (reviewed recently in 1). Transcriptionally active and silent chromatin is characterized by distinct posttranslational modifications on the histones or combinations thereof. Active genes typically carry high levels of lysine acetylation on the H3 and H4 tails, trimethylation of H3 lysine 4, trimethylation of H3 lysine 79, ubiquitylation of H2B, and trimethylation of H3 lysine 36 (Fig 1). Marks associated with repressed genes include trimethylation of lysine 27, ubiquitylation of H2A on lysine 119, and trimethylation of H3 lysine 9 (Fig 1). The chromatin-modifying enzymes that catalyze these marks can be recruited to target sites by sequence-specific DNA-binding transcription factors that regulate transcriptional states of particular genes. However, other more general features of the DNA such as its global CG content and DNA methylation status can be read by the DNA-binding Zn-finger CxxC domain present in many chromatin-modifying enzymes 2. Equally, the act of transcription can direct the recruitment of writers that associate with the transcriptional machinery, leading to the accumulation of specific marks such as H3K4me3 and H3K36me3. Figure 1. The distribution of histone modifications over active and repressed genes Download figure Download PowerPoint Given the large number of different histone modifications, the potential combinatorial complexity is vast. Advances in technology over the past decade such as ChIP-sequencing have allowed us to map the distribution and co-localization of histone marks at high-resolution genome wide, while mass spectrometry, often in combination with stable isotope labeling, enables the analysis of histone marks and dynamics at the level of a single histone tail. Interestingly, mass spectrometric data suggest that there are many combinations of modifications that are either more likely to occur together, or are mutually exclusive, suggesting crosstalk between these marks. Such crosstalk can occur in cis between distinct modifications on the same histone tail, or in trans either on neighboring histones within the same nucleosome or on neighboring nucleosomes in a chromatin domain. The patterns of histone marks associated with distinct transcriptional states are established through a dynamic interplay between histone readers, writers, and erasers. Importantly, the writers that place these marks contain chromatin-reading domains that can bind preexisting histone marks. Studies have shown that such crosstalk between histone marks can both positively and negatively regulate binding and catalytic activity of writers, resulting in positive and negative feedback loops. Therefore, writers that can also read the histone modifications are required for the establishment and maintenance of chromatin states at active and repressed genes and may play important roles in the memory and switching of gene expression states. In this review, we will focus on several examples of the positive and negative feedback mechanisms that regulate the formation, reinforcement, and maintenance of the distinct patterns of histone marks associated with active and repressed transcriptional states (Fig 2). However, such features are likely to be more general features of chromatin states, and the principles seen in these examples are likely to be applicable to the plethora of other chromatin modifications whose function is still unclear. Figure 2. Crosstalk between chromatin writers and histone marks at active and repressed genesChromatin writers and chromatin marks associated with active genes positively reinforce each other through various positive feedback mechanisms. The same holds true for writers and marks associated with repressed genes. Additionally, negative feedback mechanisms and mutual inhibition between writers and marks associated with the opposite gene expression state also reinforce distinct transcriptional states. Download figure Download PowerPoint Active histone modifications In eukaryotic organisms, gene expression is regulated through the synergistic actions of multiple factors, including but not limited to, transcription factors, the transcriptional machinery, chromatin remodelers, and the presence of specific histone variants and histone modifications. Active chromatin domains are characterized by a distinct array of histone marks. H3K27ac and H3K4me1 are associated with active enhancers 3, and high levels of H3K4me3 and H3 and H4 acetylation are found at the promoters of active genes 456. The bodies of active genes are enriched in H3 and H4 acetylation 7, H3K79me3 8, and H2BK120u1 910, and increasing H3K36me3 toward the 3′ end 11. These histone marks may regulate transcription by creating an open chromatin structure and recruit effectors that mediate a transcriptionally competent state. While the function of many active histone modifications is not fully understood, there is abundant evidence that their deposition is required for the proper regulation of gene expression. Positive crosstalk mechanisms between different histone modifications play an important role in the recruitment and maintenance of active histone modifications at active genes. Establishment and maintenance of H3K4me3 H3K4me3 is a highly conserved histone modification and its association with transcription is evolutionarily conserved in eukaryotes. In mammals, H3K4 methylation is catalyzed by six related homologs of the yeast SET1—SETD1A, SETD1B, MLL1, MLL2, MLL3, and MLL4 12. These complexes are comprised of the catalytic SETD1/MLL subunits and four core subunits WDR5, RBBP5, ASH2L, and DPY30, and as well many other complex-specific subunits 131415. H3K4me3 is a hallmark of active genes and is distributed along the promoter and TSS regions 61617. Work in yeast shows that SET1 associates with the PAF complex and the Ser5-phosphorylated initiating form of Pol II and is co-transcriptionally deposited 18 (Fig 3). Additionally, the recruitment of SETD1 and MLL to specific target genes is mediated by many cell type-specific transcription factors or transcriptional coactivators 1920212223. However in higher organisms especially, more general mechanisms of H3K4me3 recruitment and establishment are also at play. Figure 3. Establishment of H3K4me3 and interplay with H2BK120u1The SETD1 complex associates with Pol II, and H3K4me3 is deposited co-transcriptionally. CFP1 (associated with SETD1) and MLL1/2 can be recruited to promoters de novo via CxxC domain binding to CpG islands. H2BK120u1 can recruit H3K4 writers, possibly through recognition of H2BK120u1 by the ASH2L subunit. Download figure Download PowerPoint Notably, the distribution of H3K4me3 is highly coupled to the presence of CpG islands, regions of CpG- and GC-dense DNA that are predominately unmethylated and found at 50–70% of vertebrate promoters 24. A biochemical link between CpGI promoters and H3K4me3 was eluciated with the discovery of the Zn-finger CxxC domain which specifically binds nonmethylated CpGs and is present in MLL1/2 and the CFP1 subunit of SETD1A/B 2 (Fig 3). All CpGI promoters are marked with H3K4me3, and the level of H3K4me3 is correlated to gene activity 2526. Emerging evidence suggests that in vivo, MLL2 is responsible for maintaining H3K4me3 at CpGI promoters with low expression 2728, while the SETD1-specific subunit CFP1 is preferentially enriched at active gene promoters with higher levels of H3K4me3 29. In ESCs, CpGI promoters linked to developmentally regulated genes are bivalent and harbor the repressive H3K27me3 mark as well as H3K4me3 30. Importantly, it has been suggested that the ability of H3K4 writers to sample CpGIs genome wide and the presence of H3K4me3 at CpGI promoters may poise silent genes for rapid activation upon differentiation. SETD1/MLL complexes may reinforce their binding through recognition of their own mark, H3K4me3. The PHD finger domain of CFP1 is known to read H3K4me3 and mediates SETD1 interaction with H3K4me3 313233. The third PHD domain in MLL1 is important for H3K4me3 binding and MLL1 recruitment to target sites in the Hox locus 34. Other PHD domains within SETD1/MLL may also interact with H3K4me3 but remain to be further characterized 35. The ability of SETD1/MLL to sample promoters and bind H3K4me3 may be involved in the maintenance of this mark at active genes. These mechanisms of H3K4me3 binding by H3K4 writers suggest that once established, this mark may positively reinforce its own deposition. Crosstalk between H2BK120u1, H3K4me3, and H3K79me3 One of the best-studied pathways of positive histone crosstalk is the stimulation of H3K4me3 and H3K79me3 by H2BK120u1 (or H2BK123u1 in yeast). In yeast, H2BK123u1 is established by the ubiquitin ligase RAD6/BRE1 during transcriptional initiation and localizes to the TSS and along the bodies of active genes 36. Depletion of RAD6/BRE1 or mutation of H2BK123 causes severe loss of H3K4me3 and H3K79me3 3738. This positive crosstalk between H2BK123u1 and H3K4me3 and H3K79me3 is specific and does not extend to the regulation of H3K36me3, another mark associated with transcription 3738. H2BK123 lies in close proximity to H3K79 on the exposed nucleosome surface, and the H3K79 methyltransferase DOT1 in yeast has been shown to be influenced by deletion and mutation of residues on the H2B tail 39. In humans, the situation is more complex, as H3K79me3 and DOT1L distribution is not solely dependent on H2BK120u1. Human DOT1L localizes at active genes and peaks around the TSS and moreover has been shown to bind both Ser5- and Ser2-phosphorylated forms of the Pol II CTD 40. As such, H3K79me3 is a marker of active genes, yet its exact role in transcriptional regulation remains to be discovered. The crosstalk between H2BK120u1 and H3K4me3 is conserved in mammals, as knockdown of the BRE1 homologs RNF20/40 leads to global reduction in H3K4me3 41 (Fig 3). More recently, studies on the MSL1/MSL2 E3 ligase that catalyzes H2BK34u1 have also revealed a crosstalk between H2BK34u1 and H3K4me3 42. Both H2BK120u1 and H2BK34u1 are now known to allosterically stimulate the activity of the MLL complex through binding to the ASH2L subunit 43. Sites of ubiquitylation at H2BK120 and H2BK34 reside on the nucleosome surface and may provide a more favorable substrate for SET1 or MLL complex binding and activity 43. As ASH2L is a core subunit of all writers of H3K4 methylation, H2B ubiquitylation may be one mechanism of H3K4me3 maintenance at active promoters through a positive feedback loop whereby transcription results in deposition of H2Bub, which subsequently activates the H3K4 methyltransferases. H3K4me3 and histone acetylation Histone lysine acetylation is a highly abundant mark and is known to regulate many cellular processes including transcription. Acetylation of histones H3 and H4 is highly correlated with gene expression. A unique structural motif, the bromodomain, specifically recognizes acetylated lysines and is present in many proteins involved in transcriptional regulation 44. Besides the direct recruitment of effectors, histone acetylation has also been proposed to physically alter chromatin structure by neutralizing the positive charge of lysines and disrupting intra- and internucleosomal interactions, which lead to an open chromatin environment permissible to transcription. Lysine acetylation of three residues on the H3 globular domain H3K56, H3K64, and H3K122, all of which lie at the H3–DNA interface, may disrupt electrostatic interactions within the nucleosome and have been linked to gene activation 454647. H3K122ac has been shown to directly promote in vitro transcription through stimulating histone eviction 47. H3 and H4 histone tail acetylations enhance DNA unwrapping, while H3 acetylation sensitizes nucleosomes to salt-induced dissociation 48. H3K4me3 and H3/H4 acetylation coexist at the promoter and TSS of active genes, and there are many studies that suggest H3K4me3 promotes downstream H3/H4 acetylation through recruitment of HATs (Fig 4). H3K4me3 readers have been identified in many HAT complexes. SGF29, a component of the SAGA HAT complex, contains a tandem tudor domain that binds H3K4me3 and overlaps with H3K4me3 at gene promoters. SGF29 deletion causes loss of H3K9ac and loss of SAGA complex at target sites 49. Similarly, yeast NuA3 50 and NuA4 51, and mammalian HBO1 52 provide other examples of HAT complexes that contain PHD fingers that preferentially bind H3K4me3. Dynamic turnover of H3 lysine acetylation through the combinatorial action of the HAT p300/CBP and HDAC has been shown to occur on histone H3 tails with preexisting H3K4me3, but not other modifications associated with active gene expression such as H3K79me3 or H3K36me3 53. This H3K4me3-linked acetylation is conserved in higher eukaryotes including fly, mouse, and human. Loss of H3K4me3 upon CFP1 deletion leads to loss of CpGI-associated H3K9ac in ESCs 29. Further work using the Dictyostelium discoideum model shows that upon knockout of SET1 and loss of H3K4me3, dynamic H3 acetylation was lost 54. The dynamic turnover of acetylation rather than the modification itself may be key in transcriptional activation (reviewed in 55). In support of this, many members of the H3K4me3-binding PHD fingers are associated with HDACs as well as HATs 56. As H3K4me3 has been found to be promoter-associated before transcription initiation, H3K4me3-dependent co-targeting of both HATS and HDACs may facilitate the dynamic turnover of histone acetylation. The above examples illustrate that positive crosstalk between H3K4me3 and histone acetylation is an evolutionarily conserved pathway and that the cooperativity between H3K4me3 and hyperacetylation as well as the dynamic turnover of acetylation is important in ensuring proper transcriptional regulation. Figure 4. Interplay between H3K4me3, H3K36me3, and H3/H4 acetylationH3K4me3 reinforces H3 and H4 acetylation at the promoters of active genes. Various H3K36 writers catalyze H3K36me1/2 and SETD2 associates with elongating Pol II and catalyzes H3K36me3 co-transcriptionally. H3K36me2/3 recruits HDACs that deacetylate histones over gene bodies. Download figure Download PowerPoint H3K36me3 and histone deacetylation Methylation at histone H3K36 is an abundant histone mark highly conserved in eukaryotes. H3K36 mono-, di-, and trimethylation exist in yeast and all of these states are catalyzed by SET2. Mammals on the other hand have multiple writers of H3K36 methylation, including the NSD1/2/3 family, ASH1L, SMYD2, SETMAR, and SETD2, but SETD2 is the sole enzyme responsible for H3K36 trimethylation in vivo (reviewed in 57) (Fig 4). Interestingly, the uncoupling of H3K36me3 activity from H3K36me1/2 over evolution alludes to specific biologically distinct roles of each methylation state. H3K36me3 is highly correlated with the transcribed regions of active genes and levels of H3K36me3 increase toward the 3′ end of genes 11. This particular distribution results from the association of Set2 with the elongating Ser2-phosphorylated CTD of Pol II, which is predominant over the bodies and 3′ ends of active genes 585960. Like H3K4me3, H3K36me3 has also been linked to regulation of histone acetylation. H3K36me3 recruits HDACs to sites of active transcription (Fig 4). In yeast, recognition of H3K36me2/3 by the bromodomain-containing EAF3 complex recruits the HDAC RPD3S complex, which deacetylates histones and prevents spurious transcription initiation from within gene bodies 616263. H3K4me3 and histone hyperacetylation at gene promoters may regulate transcriptional initiation from the TSS, while H3K36me2/3-mediated deacetylation is required in the wake of the transcriptional machinery to prevent initiation from aberrant sites within the gene body. This mutual exclusivity of H3K4me3 and H3K36me3 may be important for maintaining transcriptional integrity. This idea is supported by work showing that promoters lack the H3K36me2/3 mark, and the H3K36me2 demethylases KDM2A/B co-localize with H3K4me3 at CpGI promoters, ensuring active removal of H3K36me2 from transcriptional start sites 6465. H3K36me2/3 is recognized by a protein motif, the PWWP domain, found in many nuclear chromatin-binding proteins 66676869. Notably, all three members of the NSD family of H3K36 methyltransferases that catalyze H3K36me1/2 each contain two PWWP domains 70 and have been shown to preferentially bind H3 peptides containing H3K36me3 69. This implies that H3K36me2/3 recognition by its writers may be important for the propagation of H3K36me1 and H3K36me2 at certain sites. Mono-/dimethylation of H3K36 is more pervasive than H3K36me3 and not restricted to sites of active transcription or euchromatin domains 7172. The biological function of mono-/dimethylation is unknown, though an increase in H3K36me2 levels as a result of mutations in NSD2 has been linked to upregulation of gene expression profiles in cancers 737475. H3K36me2 may have an important biological function in its own right or may be required to serve as a substrate for subsequent SETD2-mediated H3K36 trimethylation. The broad distribution of H3K36me2 and H3K36me3 over active chromatin may also prevent the spreading and accumulation of silencing marks such as H3K27me3 through direct inhibition of the Polycomb complex PRC2 7677, which will be discussed below. Repressive histone modifications The methylation of residues lysine 27 and lysine 9 of H3 and the ubiquitinylation of H2A on lysine 119 are hallmarks of repressive chromatin and are often found at silent gene loci. H3K27me3 and H2AK119u1 are associated with the formation of facultative heterochromatin, whereas H3K9me2/3, as well as having important roles in the formation of constitutive heterochromatin, also plays a part in regulating gene expression during development. H3K27me3 and H2AK119u1 crosstalk The Polycomb Repressive Complex 2 (PRC2) is responsible for the methylation of lysine 27 and contains four core subunits, EZH2/1, SUZ12, EED, and RBAP46/8 78. The catalytic subunit is the SET domain-containing protein EZH2 (or the related EZH1), although these enzymes are only functional in the context of the full core complex 798081. There are also accessory proteins that can associate with the core PRC2 complex to form two types of PRC2: PRC2.1 which includes a Polycomb-like subunit (PCL1/2/3) and PRC2.2 which includes the JARID2 and AEBP2 subunits 82. The function of these accessory proteins remains unclear, although they have been shown to modulate activity of PRC2 and may also play a role in targeting PRC2 to chromatin. PRC2 is able to mono-, di-, and trimethylate H3K27, although there is some dispute if PRC2 is the only H3K27me1 methyltransferase. These different methylation states have very different roles, and although H3K27me3 is linked to gene repression, recent studies have suggested that H3K27me1 may be important for gene activation and is enriched over the bodies of genes 83. The H3K27me2 modification is very prevalent in the genome, with MS/MS analysis demonstrating that it accounts for 60–80% of all nucleosomes in mESCs 84, although little is known about its function or binding proteins. H3K27me3 is the most well-characterized mark in terms of facultative heterochromatin formation and is critical for the repression of key transcriptional regulators during development. Therefore, in terms of gene silencing, we will focus on the trimethylation state of H3K27. In ES cells, H3K27me3 is present at the promoters of several thousand genes, including the Hox gene clusters, where it is associated with heritable gene silencing 85. H3K27me3 modification is also highly enriched on the inactive X chromosome suggesting a role in facultative heterochromatin formation 86. In more differentiated cell types, larger domains of H3K27me3, termed BLOCS, are often visualized over silent loci in the genome 87. As described above, for many of the enzymes associated with active gene expression, there are also positive feedback loops important for the establishment and spreading of repressive domains. The PRC2 component EED contains an aromatic cage that is able to specifically bind to H3K27me3 88. It has been shown that the binding of PRC2 to the modification it deposits is required for the full establishment of H3K27me3 domains, and such a positive feedback mechanism could also be important for the inheritance of the H3K27me3 mark through cell division 89. PRC2 has also been shown to be stimulated by dense chromatin via an interaction of the SUZ12 subunit with the H3 tail (A31-R42) 90. In this way, positive feedback from the local chromatin structure will also allow robust domains of H3K27me3 to be maintained over repressed genes. The Polycomb repressive complex 1 (PRC1) is an E3 ubiquitin ligase complex that can modify chromatin by monoubiquitylation of H2A on lysine 119. All PRC1 complexes contain the catalytic RING1A/B subunit, and one of six PCGF proteins 91. The presence of different PCGF subunits is thought to define the class of PRC1 complex, for example, PCGF2 (MEL18) and PCGF4 (BMI) make up the canonical PRC1 complexes which also contain CBX (2,4,6,7,8) and polyhomeotic subunits 92. Variant complexes include either the RYBP or YAF2 protein, the presence of which is mutually exclusive with the CBX component 9193. These variant complexes, such as the complex containing RING1B/PCGF1/RYBP/BCOR/KDM2B, have been implicated in recruitment of PRC1 and have been shown to have higher H2AK119u1 activity compared with canonical PRC1 complexes 9194. Interestingly, RYBP also contains a ubiquitin-binding domain and has been shown to bind H2AK119u1 95. This suggests that a positive reinforcement mechanism could be important to establish or maintain high levels of H2AK119u1 at PRC1 target domains, in a similar manner to PRC2 where EED binds to H3K27me3. Both PRC1 and PRC2, along with their associated chromatin modifications, H2AK119u1 and H3K27me3, have been shown to co-localize at many regions of the genome, such as the promoters of developmentally regulated genes and the inactive X chromosome 96979899. A hierarchical recruitment model, whereby the H3K27me3 modification placed by PRC2 is read by PRC1, has been proposed to explain this co-recruitment of both PRC1 and PRC2 to chromatin 100. This occurs by a specific interaction of the H3K27me3 modification with the chromodomain of the CBX protein found in canonical PRC1 complexes 101. Hence, all PRC2 targets would also become PRC1 targets and a repressive domain would be established. However, this hierarchical model is not able to account for all PRC1 recruitment to chromatin since even in the absence of PRC2, the variant RYBP-containing complexes still localize to the correct regions of the genome 93102. More recently, data from three laboratories have
Referência(s)