REVIEWS EPIGENETICS AND GENETICS Polycomb group proteins: navigators of lineage pathways led astray in cancer Adrian P. Bracken* and Kristian Helin‡ Abstract | The Polycomb group (PcG) proteins are transcriptional repressors that regulate lineage choices during development and differentiation. Recent studies have advanced our understanding of how the PcG proteins regulate cell fate decisions and how their deregulation potentially contributes to cancer. In this Review we discuss the emerging roles of long non-coding RNAs (ncRNAs) and a subset of transcription factors, which we call cell fate transcription factors, in the regulation of PcG association with target genes. We also speculate about how their deregulation contributes to tumorigenesis. Epigenetic Considerable attention is currently focused on identifying more dynamic than anticipated, showing that the PcG Relating to effects on patterns the events that lead to the development of so-called proteins are also recruited to the promoters of certain of gene expression that are ‘tumour-initiating cells’, as understanding this might genes in response to differentiation signals and, impor- heritable through cell division facilitate the design of more effective cancer therapies1–3. tantly, that this recruitment is required for their silencing and caused by mechanisms 15–19 other than changes to the It is becoming increasingly evident that, in addition to during differentiation . On the basis of these results, underlying DNA sequence. genetic alterations, tumour development involves the we and others have proposed a model in which the PcG alteration of gene expression patterns owing to epigenetic proteins function dynamically during development and Polycomb group proteins changes4. Recent studies have implicated the Polycomb differentiation to lock off the expression of alternative A group of proteins first group proteins (PcG proteins) as key contributors to these cell fate regulators in any particular lineage (FIG. 2). In described in D. melanogaster 5–9 that are required for normal changes . The PcG proteins form multiprotein repres- this Review we propose that the deregulation of these development. They work in sive complexes, called Polycomb repressive complexes mechanisms is central to tumour initiation. multiprotein complexes, called (PRCs), which repress transcription by a mechanism that Polycomb repressive probably involves the modification of chromatin (FIG. 1). PcG proteins and cancer complexes, that establish regions of chromatin in which Several genetic studies in different organisms have The PcG proteins are essential for the maintenance of 20–22 gene expression is repressed. firmly established the vital and conserved roles for PcG both normal and cancer stem cell populations . This proteins in embryonic development and adult somatic is partly attributed to their ability to bind to and repress cell differentiation10. Moreover, recent studies have dem- the CDKN2B and CDKN2A loci, which encode the tumour onstrated that the PcG proteins are required for main- suppressors INK4B (encoded by CDKN2B), INK4A and taining the correct identities of stem, progenitor and ARF (both encoded by CDKN2A)21,23–31. INK4A and differentiated cells11. The genome-wide mapping of PcG INK4B function upstream in the RB pathway, and ARF target genes in mammalian cells has offered scientists the functions upstream in the p53 pathway25,32. In addition to opportunity to start to unravel the molecular mechanisms frequent genetic alterations, this locus is often epigeneti- *The Smurfit Institute of of PcG protein action12–14. The PcG proteins have been cally silenced by DNA methylation in cancer, and the PcG Genetics, Trinity College 26 Dublin and The Adelaide & found to bind and repress the promoters of genes that proteins have been proposed to contribute to this . Many Meath Hospital, including the encode proteins with key roles in cell fate determination additional PcG target genes accumulate DNA methylation National Children’s Hospital, in many different cellular lineages. Although these data on their promoters in cancer, such as Wilm’s tumour 1 Dublin, Ireland. support the large body of evidence that points to crucial (WT1), retinoic acid receptor-β (RARB), kruppel-like ‡Biotech Research and Innovation Centre (BRIC) and roles for the PcG proteins in both development and adult factor 4 (KLF4), inhibitor of DNA binding 4 (ID4), GATA Centre for Epigenetics, homeostasis, we are only beginning to understand how binding protein 3 (GATA3) chromodomain helicase University of Copenhagen, the PcG proteins actually regulate their target genes. DNA binding protein 5 (CHD5) and PU.1 (also known as Copenhagen 22009, Initial studies have established that the PcG proteins SPI1)13. The reports that enhancer of zeste homologue 2 Denmark. are displaced from certain target genes, for example the (EZH2)33 and chromobox homologue 7 (CBX7)34 can e-mails: homeobox (Hox) genes DNA methyltransferases [email protected]; , on their transcriptional activation physically associate with (DNMTs) 13–15 [email protected] during differentiation . However, subsequent studies suggest a mechanism whereby the PcG proteins directly doi:10.1038/nrc2736 demonstrated that the binding of PcG proteins is much contribute to the altered DNA methylation profiles that NATURE REVIEWS | CANCER VOLUME 9 | NOVEMBER 2009 | 773 © 2009 Macmillan Publishers Limited. All rights reserved REVIEWS A t a glance Review we discuss an alternative and complementary hypothesis in which PcG proteins are led astray in cancer • The Polycomb group (PcG) proteins regulate cell fate decisions during development by the deregulation of factors that are required for their and differentiation. They form multiprotein repressive complexes called Polycomb association to target genes. We propose that the deregu- repressive complexes (PRCs), which modify chromatin. lation of these factors directly contributes to the aberrant • The PcG proteins bind and repress the promoters of hundreds of genes encoding modulation of transcriptional programmes observed in proteins with roles in cell fate determination. many cancers. • It is unclear how PcG proteins are displaced and recruited to different subsets of target genes during cell fate decisions. However, cell fate transcription factors PcG recruitment to target genes (CFTFs) and long non-coding RNAs (ncRNAs) are emerging as potential regulators. PcG proteins do not have the ability to bind specific • There is growing evidence that many PcG target genes are silenced in advanced DNA motifs. Therefore, a key mechanistic question cancer and that this may be the result of an epigenetic switch to DNA methylation concerns how they are recruited to and displaced from during neoplastic progression. their target genes during lineage specification. The • Several PcG proteins are known to be deregulated in cancer. We propose that the answer to this question not only has implications for our deregulation of CFTFs and long ncRNAs also leads to the misexpression of PcG fundamental understanding of lineage choice during target genes. development and differentiation, but may also consid- erably contribute to our understanding of the initiating events in cancer. are observed in multiple cancer types. In fact, PcG target genes are as much as 12 times as likely to be aberrantly Transcription factors recruit PcG proteins. In Drosophila silenced by DNA methylation in cancer as non-PcG target melanogaster, several transcription factors are required genes7–9, and poorly differentiated and aggressive human to recruit PcG proteins to polycomb repressive elements Homeobox (Hox) genes 6 51 Genes encoding a group of tumours show preferential repression of PcG target genes . (PREs) during development . One such transcription transcription factors that Taken together, these results suggest a possible scenario in factor, encoded by Yy1 (also known as Pho), has recently specify the anterior–posterior which PcG proteins and DNA methylating enzymes (such been shown to co-occupy most PREs with PRC1 and axis and segment identity of as DNMTs) cooperate to aberrantly silence pro-differen- PRC2 components in D. melanogaster embryos and metazoan organisms during 19,52 early embryonic development. tiation and anti-proliferative genes, which leads to the larvae . The PRE in D. melanogaster is not an easily accumulation of a population of cells unable to respond recognizable DNA sequence motif as it is not a single CDKN2B and CDKN2A loci to differentiation signals. It is thought that the consequent transcription factor binding site. Instead, it is a collec- A stretch of 45 kb of block of differentiation may allow these tumour-initiating tion of binding sites, defined as an ‘element’ of several chromosome 9 (in humans), cells to linger and accumulate the additional epigenetic hundred base pairs. To date, PREs have not been defined which is frequently the target of mutation, deletion and and/or genetic alterations necessary to develop into in mammalian cells, despite the mapping of several thou- 12–14 epigenetic silencing in cancer. a tumour. sand binding sites for the PcG proteins . This suggests They encode three tumour However, a key question remains unanswered: what that many different mammalian transcription factors suppressor proteins: INK4A triggers the aberrant silencing of PcG target genes that is contribute to the recruitment of the PcG proteins. In and INK4B, which function in the RB pathway, and ARF, which observed in many cancer types? One