Project : The Polycomb and Trithorax page
In this page you will find basic information on Polycomb and Trithorax proteins in epigenetic regulation; as well as the teaching material of our lab on this and related subjects. This teaching material can be downloaded and used without need of permission, but please cite this web publication address as the source of information in order to allow users to address us enquiries and correspondence.
You will also find some links to relevant papers in the Polycomb and Trithorax field, and to Web sources of information in this subject. Enjoy polycomb!
Polycomb history and introduction
Polycomb group (PcG) and trithorax group (trxG) proteins regulate expression patterns of many developmental genes. Their function is best understood in the regulation of homeotic genes, where these proteins are able to maintain, respectively, silenced or active states throughout development. These proteins raised considerable interest in recent years, both because the basic regulatory mechanisms that involve these factors are fascinating, and because they play key roles in a variety of normal cellular processes and in disease.
A brief introduction to Polycomb and Trithorax
Polycomb group (PcG) proteins are highly conserved regulatory factors that were initially discovered in Drosophila. PcG genes are best known for their role in maintaining silent expression states of Hoxgenes during development, while trithorax group (trxG) proteins maintain Hox gene expression patterns in the appropriate spatial domains. PcG and trxG proteins are also involved in the regulation of normal cell proliferation, and their mutation has been linked to defects in stem cell fates and to cancer. They act by regulating chromatin structure and chromosome architecture at their target loci.
PcG proteins form multimeric complexes that exert their functions by modifying chromatin structure and by regulating the deposition and recognition of multiple post-translational histone modifications. Three major PcG protein complexes have been described. The first, named PhoRC, contains the DNA-binding protein Pho (this is the Drosophila name, the homolog in mammals is YY1). The second complex, named the E(Z)/ESC complex or Polycomb Repressive Complex 2 (PRC2), contains four core proteins: the histone methyltransferase Enhancer of Zeste (E(Z)), Extra sex combs (ESC), Suppressor of zeste-12 (SU(Z)12), and nucleosome-remodeling factor 55 (NURF-55). E(Z) trimethylates lysine 27 of histone H3 (H3K27me3), and, to a lesser extent, lysine 9 of histone H3 (H3K9me3). A third complex, named PRC1, recognizes these methylation marks via the chromodomain of the Polycomb (PC) protein. PC is a stoichiometric component of PRC1, together with Polyhomeotic (PH), Posterior Sex Combs (PSC), and dRING. In mammals, the duplication of many PcG genes allows variations in complex composition, which differ with cell type and developmental stage.
TrxG proteins are a somewhat heterogeneous group, but they are characterized by complementary mechanistic properties to the PcG. Within trxG members, some bind specific sequences of DNA. A second class class of trxG members is composed by SET domain factors like Drosophila Trx and Ash1 and vertebrate MLL, as well as their associated proteins. A third class of trxG factors comprises protein components of ATP-dependent chromatin remodeling complexes like the SWI/SNF or the NURF complexes, and includes proteins (such as one component of the NURF complex) specifically capable to "read" the histone methylation marks laid down by the SET domain proteins.
In Drosophila, PcG proteins repress their target genes by binding to specific DNA elements called Polycomb Response Elements (PREs). Analysis of known PREs has revealed the presence of binding sites (usually in multiple copies) for several DNA-binding proteins, such as Pleihomeotic (PHO) and Pleihomeotic-like (PHOL), GAGA factor (GAF)/Pipsqueak (PSQ), Zeste and DSP. Other studies have suggested possible additional roles for other proteins, such as the corepressor CtBP and the DNA binding factors Grainyhead (GRH) as well as members of the Sp1/KLF family. Therefore, a large number of proteins might contribute to PcG recruitment at PREs. Each PRE has a different number and topological organization of binding sites for these factors, possibly providing the basis for the specificity of PRE function.
PREs have only been characterized in Drosophila so far. In general, PREs might be simply defined as DNA elements necessary and sufficient for recruitment of PcG complexes and for PcG-dependent silencing of flanking promoters. Many of the PcG binding sites identified by chromatin immunoprecipitation in vertebrates might correspond to this criterion. Their DNA sequences are likely to be fairly different from fly PREs, since three of the DNA-binding factors involved in PcG recruitment, GAF, Pipsqueak and Zeste, are not conserved in vertebrates. Indeed, CpG islands can by themselves recruit Polycomb complexes if not methylated.
In addition to modifications at the chromatin level, regulation at the level of nuclear architecture influences the regulation of PcG target genes. In mice, it has been reported that nuclear re-organization is coupled to Hox gene activation in early development. In Drosophila, homologous chromosomes pair in interphase nuclei, and transgenic PREs typically silence more strongly when they are present in two copies on homologous chromosomes. This notion of pairing is reinforced by the finding that PRE-containing sequences can also pair with homologous sequences located on different chromosomes, and that these long distance nuclear interactions reinforce PcG-mediated silencing.
Therefore, multiple mechanisms cooperate to drive regulation of gene expression by PcG and trxG proteins. This is likely very important in light of the fact that these proteins regulate a large number of genes, sometimes maintaining the memory of transcriptionalstates, while in other cases their regulation is more flexible. These multiple mechanisms may be important to ensure the necessary regulatory plasticity, while providing sufficient robustness to the regulated state.
Recent reviews for further readings
- Schuettengruber, B., Bourbon, H.M., Di Croce, L., and Cavalli, G.
Genome Regulation by Polycomb and Trithorax: 70 Years and Counting.
Cell 2017 171, 34-57. doi: 10.1016/j.cell.2017.08.002.
PMID: 28938122 - Piunti, A., Shilatifard, A.
Epigenetic balance of gene expression by Polycomb and COMPASS families.
Science 2016, 352(6290):aad9780, doi:10.1126/science.aad9780. PMID: 27257261 - Koppens M, van Lohuizen, M
Context-dependent actions of Polycomb repressors in cancer
Oncogene 2015, doi:10.1038/onc.2015.195. Epub ahead of print - Sexton T, Cavalli, G
The role of chromosome domains in shaping the functional genome
Cell 2015, 160: 1049-1059 - Lanzuolo C, Orlando V.
Memories from the polycomb group proteins
Annu Rev Genet. 2012;46:561-89. doi: 10.1146/annurev-genet-110711-155603. Epub 2012 Sep 17.
PMID: 22994356 - Pirrotta V, Li HB.
A view of nuclear Polycomb bodies.
Curr Opin Genet Dev. 2012 Apr;22(2):101-9. doi: 10.1016/j.gde.2011.11.004. Epub 2011 Dec 16. Review.
PMID: 22178420 [PubMed - indexed for MEDLINE] - Holec S, Berger F
Polycomb group complexes mediate developmental transitions in plants.
Plant Physiol. 2012 Jan;158(1):35-43. doi: 10.1104/pp.111.186445. Epub 2011 Nov 15. Review. No abstract available.
PMID: 22086420 [PubMed - indexed for MEDLINE] - Bantignies F, Cavalli G
Polycomb group proteins: repression in 3D.
Trends Genet. 2011 Nov;27(11):454-64. doi: 10.1016/j.tig.2011.06.008. Epub 2011 Jul 25. Review.
PMID: 21794944 [PubMed - indexed for MEDLINE] - Schuettengruber B, Martinez AM, Iovino N, Cavalli G.
Trithorax group proteins: switching genes on and keeping them active.
Nat Rev Mol Cell Biol. 2011 Nov 23;12(12):799-814. doi: 10.1038/nrm3230. Review.
PMID: 22108599 [PubMed - indexed for MEDLINE] - Margueron R, Reinberg D.
The Polycomb complex PRC2 and its mark in life.
Nature. 2011 Jan 20;469(7330):343-9. doi: 10.1038/nature09784. Review.
PMID: 21248841 [PubMed - indexed for MEDLINE] - Mills AA.
Throwing the cancer switch: reciprocal roles of polycomb and trithorax proteins.
Nat Rev Cancer. 2010 Oct;10(10):669-82. doi: 10.1038/nrc2931. Review.
PMID: 20865010 [PubMed - indexed for MEDLINE] - Sauvageau M, Sauvageau G.
Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer.
Cell Stem Cell. 2010 Sep 3;7(3):299-313. doi: 10.1016/j.stem.2010.08.002. Review.
PMID: 20804967 [PubMed - indexed for MEDLINE] - Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G.
Genome regulation by polycomb and trithorax proteins.
Cell. 2007 Feb 23;128(4):735-45.
PMID: 17320510 [PubMed - in process]
Polycomb and trithorax group proteins
This table lists PcG and trxG proteins in humans and flies, as well as proteins that may be involved at recruiting them to their target genes. The genes are hyperlinked to the corresponding databases, either Flybase or Ensembl (for Human links). When multiple genes correspond to one entry (for instance, there are 5 possible human Proteins that can elicit the function of fly Polycomb), only the link to the first of the possible member are given. The other ones can be found by searching in Ensembl or HGNC databases).
Note: This table is constantly under revision. should you see mistakes or have updates, please send me an email
* indicates that the protein exist but its function in the PcG or trxG pathway is still not clear
| PcG/trxG recruiters | Drosophila melanogaster | Homo sapiens | Notes |
|---|---|---|---|
| Dsp1 | HMGB2 | Dsp1 is an HMG box protein. It assists Pho in PcG recruitment at Drosophila PREs. HMGB2 is involved in YY1 in silencing of D4Z4 repeats |
|
| Grh | GRHL1 | Fly Grh helps PcG recruitment at one PRE | |
| Gaga factor / Trl | ? | Fly Trl is involved for PcG recruitment at some PREs although is classified as a trxG protein. It is a Zn-finger sequence specific protein that binds the GAGAG motif. It also contains a BTP/POZ domain that is generally involved in protein-protein interactions | |
| Lolal | ? | Lola-like binds Trl and acts as a PcG protein | |
| Psq | ? | Psq co-purifies with components of the PRC1 complex and binds the same sequences as Trl | |
| Zeste | ? | Zeste found within PRC1 but also linked to trxG-mediated activation | |
| Fly PhoRC complex Identified in 2006 |
Fly PhoRC binds PREs and is involved in recruitment of PcG proteins to PREs. Pho also forms a second complex named INO80, likely to be involved in chromatin remodelling. Pho can recruit the histone methyltransferase E(z) to the Ubx PRE. In vitro, it can also recruit PRC1 components to DNA independent on the action of E(z). Whether PhoRC exist in human cells is unknown, but its homolog YY1 ca, recruit PcG proteins to target genes |
||
| ? | E2F6 | E2F6 forms two different multimeric complexes containing PcG proteins, one with RING1A, RING1B and MBLR, and the other one with EZH2, E(PC) and Sin3A | |
| ? | BCL6 | BCL6 is a BTB containing protein (similar to Drosophila Krüppel, but it is not known whether it is a true homolog) that was suggested to recruit PcG proteins to its target genes via the corepressor BCOR complex | |
| Rbf | RB1 RBL1 |
Human Retinoblastoma protein represses genes in a PcG-dependent manner to block cell proliferation. This pathway was not yet identified in other organisms | |
| ? | PLZF | PLZF has been shown to bind to the HoxD complex and to bind Polycomb proteins on chromatin. This sequence specific DNA binding protein contains a Zn-Finger domain and a BPB/POZ domain that is generally involved in protein-protein interactions. Plzf mutants strongly derepress the HoxD locus in the embryonic hindlimb bud, PLZF binds to Bmi-1 and recruits it to HoxD |
| PcG complexes | PcG complex components | Characteristic Domain | (Epigenetic) Function | |
|---|---|---|---|---|
| Mammals | Flies | |||
| core PRC1 complex | RING1A/B | dRing/Sce | RING finger domain | H2AK119 ubiquitylation |
| PCGF1-6 | Psc/Suz(2) | RING finger domain, UBL (RAWUL) domain | H2AK119 ubiquitylation, oligomerization | |
| canonical PRC1 | CBX2,4,6-8 | Pc | Chromo domain | H3K27me3 binding |
| PHC1-3 | Ph-p/Ph-d | Sterile alpha motif (SAM) domain | oligomerization/protein-protein interation | |
| SCMH1/2 | Scm | SAM domain | oligomerization/protein-protein interation | |
| non-canonical PRC1 | RYBP/YAF2 | Rybp | Zinc finger domain | DNA binding |
| KDM2B | Kdm2 | JmjC domain, CxxC domain | H3K36 demethyalse, DNA binding | |
| DCAF7 | Wap | WD40 domain | scaffold factors | |
| WDR5 | Wds | WD40 domain | scaffold factors | |
| core PRC2 complex | EZH1/2 | E(z) | SET domain, SANT domain | H3K27 methyltransferase, histone binding |
| SUZ12 | Suz(12) | Zinc finger domain | RNA/DNA binidng | |
| EED | Esc/Escl | WD40 domain | H3K27me binding | |
| RBBP4/7 | Nurf55/Caf1 | WD40 domain | H3K36me3 binding | |
| PRC2 accessory proteins | PCL1-3 | Pcl | Tudor domain; PHD-finger domain | H3K36me3 binding |
| JARID2 | Jarid2 | Zinc finger domain, ARID domain | H2Aub binding, RNA binding | |
| AEBP2 | Jing | Zinc finger domain | DNA binding, H2Aub binding | |
| EPOP/C17orf96 | modulating enzymatic activity | |||
| LCOR/C10orf12 | unknown | |||
| core PR-DUB | BAP1 | Calypso | biquitin carboxyl-terminal hydrolase (UCH) N-terminus catalytic domain | Ubiquitin carboxyl-terminal hydrolase |
| ASXL1/2 | Asx | chromatin binding | ||
| PR-DUB accessory proteins | FOXK1/2 | FoxK | Forkhead box | DNA binding |
| OGT | Sxc | O-GlcNAcylation | ||
| KDM1B | dLsd1 | amine oxidase domain | Histone demethylation | |
| MBD5/6 | Sba | methyl binding domain | DNA binding | |
| trxG complexes | trxG complex components | Protein Domain | (Epigenetic) Function | |
| core COMPASS components | WDR5 | Wds | WD40 domain | Histone binding |
| ASH2L | Ash2 | Zinc finger domain | DNA binding | |
| RBBP5 | Rbbp5 | WD40 domain | Histone binding | |
| DPY30 | Dpy30 | |||
| SET1/COMPASS | SET1A/B | dSet1 | SET domain | H3K4 methyltransferase |
| HCFC1 | Hcf1 | Kelch domain | ||
| WDR82 | Wdr82 | WD40 domain | Histone binding | |
| CFP1 | Cfp1 | CxxC domain | DNA binding | |
| MLL1/2 COMPASS-like | MLL1/2 | Trx | SET domain | H3K4 methyltransferase |
| HCFC1 | Hcf1 | Kelch domain | ||
| MENIN | Menin | |||
| MLL3/4 COMPASS-like | MLL3/4 | Trr | SET domain | H3K4 methyltransferase |
| NCOA6 | Ncoa6 | |||
| PAGR1 | Pa1 | |||
| UTX | Utx | JmjC domain | H3K27 demethylase | |
| PTIP | Ptip | BRCT domain | ||
| ASH1 | ASH1L | Ash1 | SET domain; Bromo domain | H3K36 mehyltransferase |
| CBP | dCbp | HAT domain; Bromo domain | H3K27 acetyltransferase | |
| SWI/SNF (BAF and PBAF) complex | BRM/BRG1 | Brm | Helicase, Bromo domain | ATPase-dependent chromatin remodlling |
| BAF250A/B | Osa | ARID domain | possible DNA binding | |
| BAF155/170 | Mor | SWIRM, SANT, Chromo domain | possible DNA and histone binding | |
| BAF47 | Snr1 | Winged helix domain | possible DNA binding | |
| BAF45A-D | Sayp | PHD-finger domain | possible DNA binding | |
| BAF53A/B | Bap55 | Actin-like | ||
| BAF180/BAF200 | polybromo | Polybromodomain | histone binding | |
| BAF60A-C | Bap60 | Swi-B domain | ||
| BAF57 | Bap111 | HMG domain | possible DNA binding | |
| beta-ACTIN | Actin5C | |||
| BCL7A-C | Bcl7-like | |||
| BRD7/9 | CG7154 | |||
List of landmark discoveries in the Polycomb and Trithorax field
| Year | Brief description of the main findings | Pubmed link |
|---|---|---|
| 1978 | Ed Lewis's founding Polycomb paper identifying a role for the Pc gene in the regulation of homeotic genes | go! |
| 1985 | Characterization of the trithorax gene as a regulator of homeotic gene expression Role of PcG proteins in the maintenance of homeotic gene expression, i.e. in the process of "cellular memory" |
go! go! |
| 1988 | Antagonism between Polycomb and trithorax genes | go! |
| 1989 | Polytene chromosome binding pattern of Pc | go! |
| 1991 | Identification of Bmi-1, the first mammalian PcG gene Role of Bmi-1 in Cancer |
go! go: a! b! |
| 1992 | Involvement of Trithorax in leukemia | go! |
| 1993 | Characterization of PREs in Drosophila Chromatin IP of Polycomb |
go: a! b! c! go! |
| 1994 | Bmi-1 action as a bona fide mammalian PcG protein | go! |
| 1997 | Analysis of PcG proteins in plants PcG proteins and epigenetic regulation of gene expression by "cosuppression" |
go! go! |
| 1999 | Purification of the PRC1 complex Role of PcG in cell proliferation |
go! go! |
| 2000 | trxG proteins and histone acetylation | go: a! b! |
| 2001 | Link between PcG proteins and the basal transcriptional machinery PcG proteins and genomic imprinting in mammals |
go: a! b! go! |
| 2002 | Characterization of the E(z)-Esc / PRC2 complex - Histone methyltransferase activity trxG proteins and histone methylation |
go: a! b! c! d! go: a! b! |
| 2003 | Binding of the PC chromo domain to histone H3 methylated at Lysine 27 PcG proteins and X-inactivation Polycomb as a Sumo E3 protein |
go: a! b! go: a! b! go! |
| 2004 | PRC1 proteins mediate histone ubiquitination Identification of a PRC3 complex related to PRC2 and identification of histone H1 methylation activity |
go! go! |
| 2005 | Identification of a link between PcG proteins and DNA methylation Role for PcG proteins in the phenomenon of transdetermination in Drosophila |
go: a! b! go: a! b! |
| 2006 | Genome-wide mapping of the downstream target sites for PcG proteins | Drosophila: a! b! c! Human Mouse |
| 2007 | Discovery of H3K27me3 demethylases | a! b! c! d! |
| 2009 | 1- Crystal structure of EED reveals a mechamism for maintenance of H3K27me3 through the cell cycle (partially supports an earlier work by the Helin lab) 2- Identification and initial characterization of the first mammalian PREs |
1a!1b! 2a!2b! |
| 2010 | Various links between PcG proteins and noncoding RNAs (earlier work had pointed to a link between PcG proteins and a ncRNA in X inactivation, but in 2010 the data were broadly generalized and, in particular, SUZ12 was shown to be an RNA-binding protein. | a! b! c! d! |
| 2012 | Identification of alternate mammalian PRC1 complexes, suggesting that each of them may have specific functions | a! b! c! |
| 2014 | Discovery of a role for Histone H2A ubiquitylation in the recruitment of PRC2 complexes | go |
| 2015 | Discovery of a network of Polycomb-target genes in the cell nucleus of mammalian organisms | a!b! |
| 2017 | Mechanisms of SWI/SNF (BAF) complex-mediated eviction of Polycomb complexes in normal cells and cancer | a! b! |
| For obvious reasons, this list does not include the work in our lab. For this, please go to the lab main page. Moreover, this list is certainly not perfect. If you have important additions or updates that you wish to be included, please write me an email. | ||
Montpellier teaching
Below, you find teaching courses specifically given to Montpellier students.
- UE Méthodologie, a course for Montpellier students on: in vivo protein-DNA interactions (ChIP, DamID, 3C, 4C, HiC...)
course held in February 2017. Download - Master 1 - UE Génomique fonctionnelle
course held in September 2016. Download - Master 2 - Biologie du Developpement-Cellules souches-Biothérapie
course held in December 2016. Download - Master 2R - TC1 (HMBS324) « Genetic and epigenetic information - molecular bases »
course held in Autumn 2016. Download - Master 2R - (HMBS204) - Systems biology / Biologie des systèmes
course held in Autumn 2017. Download Cavalli - Download Jost