PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 (CCND2) oncogene

Polycomb group proteins are essential epigenetic repressors. They form multiple protein complexes of which two kinds, PRC1 and PRC2, are indispensable for repression. Although much is known about their biochemical properties, how mammalian PRC1 and PRC2 are targeted to specific genes is poorly understood. Here, we establish the cyclin D2 (CCND2) oncogene as a simple model to address this question. We provide the evidence that the targeting of PRC1 to CCND2 involves a dedicated PRC1-targeting element (PTE). The PTE appears to act in concert with an adjacent cytosine-phosphate-guanine (CpG) island to arrange for the robust binding of PRC1 and PRC2 to repressed CCND2. Our findings pave the way to identify sequence-specific DNA-binding proteins implicated in the targeting of mammalian PRC1 complexes and provide novel link between polycomb repression and cancer.

[1]  D. Dorsett,et al.  Polycomb repressive complex 1 modifies transcription of active genes , 2017, Science Advances.

[2]  K. Helin,et al.  Maintaining cell identity: PRC2-mediated regulation of transcription and cancer , 2016, Nature Reviews Cancer.

[3]  S. Sati,et al.  Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development , 2016, Nature Genetics.

[4]  Y. Schwartz,et al.  Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements , 2016, Nucleic acids research.

[5]  Luciano Di Croce,et al.  The dynamic interactome and genomic targets of Polycomb complexes during stem cell differentiation , 2016, Nature Structural &Molecular Biology.

[6]  M. Lohuizen,et al.  Context-dependent actions of Polycomb repressors in cancer , 2016, Oncogene.

[7]  Daniel R. Zerbino,et al.  Ensembl 2016 , 2015, Nucleic Acids Res..

[8]  Robert S Illingworth,et al.  The E3 ubiquitin ligase activity of RING1B is not essential for early mouse development , 2015, Genes & development.

[9]  R. Paro,et al.  Trithorax and Polycomb group-dependent regulation: a tale of opposing activities , 2015, Development.

[10]  Jürg Müller,et al.  Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation , 2015, Genes & development.

[11]  A. Taherbhoy,et al.  BMI1–RING1B is an autoinhibited RING E3 ubiquitin ligase , 2015, Nature Communications.

[12]  Yuri B Schwartz,et al.  Genome-wide activities of Polycomb complexes control pervasive transcription , 2015, Genome research.

[13]  D. Pasini,et al.  The controversial role of the Polycomb group proteins in transcription and cancer: how much do we not understand Polycomb proteins? , 2015, The FEBS journal.

[14]  D. Reinberg,et al.  An AUTS2–Polycomb complex activates gene expression in the CNS , 2014, Nature.

[15]  B. Garcia,et al.  Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia. , 2014, Blood.

[16]  K. Helin,et al.  Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. , 2014, Molecular cell.

[17]  Lukas Burger,et al.  Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation , 2014, Proceedings of the National Academy of Sciences.

[18]  R. Kingston,et al.  H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex , 2014, eLife.

[19]  Y. Schwartz,et al.  Combinatorial Interactions Are Required for the Efficient Recruitment of Pho Repressive Complex (PhoRC) to Polycomb Response Elements , 2014, PLoS genetics.

[20]  N. Brockdorff,et al.  Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation , 2014, Cell.

[21]  Tiziana Bonaldi,et al.  Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity. , 2014, Molecular cell.

[22]  Y. Schwartz,et al.  A new world of Polycombs: unexpected partnerships and emerging functions , 2013, Nature Reviews Genetics.

[23]  D. Duboule,et al.  A Genetic Approach to the Recruitment of PRC2 at the HoxD Locus , 2013, PLoS genetics.

[24]  Ilya Ioshikhes,et al.  Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors , 2013, Nucleic acids research.

[25]  D. Dorsett,et al.  Cohesin and Polycomb Proteins Functionally Interact to Control Transcription at Silenced and Active Genes , 2013, PLoS genetics.

[26]  K. Hahn,et al.  An orally bioavailable chemical probe of the Lysine Methyltransferases EZH2 and EZH1. , 2013, ACS chemical biology.

[27]  N. Brockdorff Noncoding RNA and Polycomb recruitment. , 2013, RNA.

[28]  K. Helin,et al.  Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. , 2013, Molecular cell.

[29]  H. Jäckle,et al.  A Histone Mutant Reproduces the Phenotype Caused by Loss of Histone-Modifying Factor Polycomb , 2013, Science.

[30]  D. Zheng,et al.  An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. , 2013, Molecular cell.

[31]  Mikhail Pachkov,et al.  Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting , 2013, Genome research.

[32]  C. Ponting,et al.  KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands , 2012, eLife.

[33]  Yang Shi,et al.  Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity , 2012, Nature Structural &Molecular Biology.

[34]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[35]  Ruedi Aebersold,et al.  Molecular architecture of human polycomb repressive complex 2 , 2012, eLife.

[36]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[37]  I. Ioshikhes,et al.  Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor , 2012, Nucleic acids research.

[38]  F. Pettersson,et al.  Sequence signatures involved in targeting the male-specific lethal complex to X-chromosomal genes in Drosophila melanogaster , 2012, BMC Genomics.

[39]  N. Tommerup,et al.  REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells , 2012, PLoS genetics.

[40]  N. Brockdorff,et al.  RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3 , 2012, Cell.

[41]  Yuval Kluger,et al.  PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. , 2012, Molecular cell.

[42]  Candace R. Chouinard,et al.  Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors. , 2012, Molecular cell.

[43]  J. Hughes,et al.  An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment , 2012, The EMBO journal.

[44]  Li-Ling Chak,et al.  Human Wharton’s Jelly Stem Cells Have Unique Transcriptome Profiles Compared to Human Embryonic Stem Cells and Other Mesenchymal Stem Cells , 2011, Stem Cell Reviews and Reports.

[45]  Prashanth Athri,et al.  Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. , 2011, Genome research.

[46]  Bradley E. Bernstein,et al.  GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells , 2010, PLoS genetics.

[47]  Shili Duan,et al.  Recognition and Specificity Determinants of the Human Cbx Chromodomains* , 2010, The Journal of Biological Chemistry.

[48]  H. Clevers,et al.  Cyclin D2-cyclin-dependent kinase 4/6 is required for efficient proliferation and tumorigenesis following Apc loss. , 2010, Cancer research.

[49]  Lars Hennig,et al.  Regulation of cell identity by plant Polycomb and trithorax group proteins. , 2010, Current opinion in genetics & development.

[50]  Luca Mazzarella,et al.  Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators , 2010, Nature Cell Biology.

[51]  Juri Rappsilber,et al.  JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells , 2010, Nature.

[52]  Gang Li,et al.  Jarid2 and PRC2, partners in regulating gene expression. , 2010, Genes & development.

[53]  P. Park,et al.  A Region of the Human HOXD Cluster that Confers Polycomb-Group Responsiveness , 2010, Cell.

[54]  Per Stenberg,et al.  Alternative Epigenetic Chromatin States of Polycomb Target Genes , 2010, PLoS genetics.

[55]  S. Orkin,et al.  Jumonji Modulates Polycomb Activity and Self-Renewal versus Differentiation of Stem Cells , 2009, Cell.

[56]  Arend Sidow,et al.  Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells , 2009, Cell.

[57]  H. Lipshitz,et al.  A Vertebrate Polycomb Response Element Governs Segmentation of the Posterior Hindbrain , 2009, Cell.

[58]  P. Yaswen,et al.  A Versatile Viral System for Expression and Depletion of Proteins in Mammalian Cells , 2009, PloS one.

[59]  Amos Tanay,et al.  Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos , 2009, PLoS biology.

[60]  Hengbin Wang,et al.  Role of hPHF1 in H3K27 Methylation and Hox Gene Silencing , 2007, Molecular and Cellular Biology.

[61]  Jean-Stéphane Varré,et al.  Efficient and accurate P-value computation for Position Weight Matrices , 2007, Algorithms for Molecular Biology.

[62]  W. Kamps,et al.  Evidence Based Selection of Housekeeping Genes , 2007, PloS one.

[63]  Kristian Helin,et al.  The Polycomb group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells. , 2007, Genes & development.

[64]  Daniel Chourrout,et al.  Genome Regulation by Polycomb and Trithorax Proteins , 2007, Cell.

[65]  Anke Sparmann,et al.  Polycomb silencers control cell fate, development and cancer , 2006, Nature Reviews Cancer.

[66]  Yuri B Schwartz,et al.  Polycomb Complexes and the Propagation of the Methylation Mark at the Drosophila Ubx Gene* , 2006, Journal of Biological Chemistry.

[67]  Jürg Müller,et al.  Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. , 2006, Genes & development.

[68]  Kristian Helin,et al.  Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. , 2006, Genes & development.

[69]  Richard Bourgon,et al.  Genome-wide analysis of Polycomb targets in Drosophila melanogaster , 2006, Nature Genetics.

[70]  C. Allis,et al.  Mouse Polycomb Proteins Bind Differentially to Methylated Histone H3 and RNA and Are Enriched in Facultative Heterochromatin , 2006, Molecular and Cellular Biology.

[71]  Haruhiko Koseki,et al.  Mammalian Polyhomeotic Homologues Phc2 and Phc1 Act in Synergy To Mediate Polycomb Repression of Hox Genes , 2005, Molecular and Cellular Biology.

[72]  S. Walfisch,et al.  Expression of D-type cyclins in colon cancer and in cell lines from colon carcinomas , 2005, British Journal of Cancer.

[73]  Anders Berglund,et al.  Sequence signature analysis of chromosome identity in three Drosophila species , 2005, BMC Bioinformatics.

[74]  S Miyano,et al.  Open source clustering software. , 2004, Bioinformatics.

[75]  M. Pfaffl,et al.  Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations , 2004, Biotechnology Letters.

[76]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[77]  Julio E. Agno,et al.  Cyclin D2 and p27 Are Tissue-Specific Regulators of Tumorigenesis in Inhibin α Knockout Mice , 2003 .

[78]  Youngchang Kim,et al.  Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. , 2003, Genes & development.

[79]  D. Reinberg,et al.  Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. , 2002, Genes & development.

[80]  V. Pirrotta,et al.  Drosophila Enhancer of Zeste/ESC Complexes Have a Histone H3 Methyltransferase Activity that Marks Chromosomal Polycomb Sites , 2002, Cell.

[81]  Brigitte Wild,et al.  Histone Methyltransferase Activity of a Drosophila Polycomb Group Repressor Complex , 2002, Cell.

[82]  Hengbin Wang,et al.  Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing , 2002, Science.

[83]  J. Hodgson,et al.  Site-Specific Recognition of a 70-Base-Pair Element Containing d(GA)n Repeats Mediatesbithoraxoid Polycomb Group Response Element-Dependent Silencing , 2001, Molecular and Cellular Biology.

[84]  M. Vidal,et al.  Mice doubly deficient for the Polycomb Group genes Mel18 and Bmi1 reveal synergy and requirement for maintenance but not initiation of Hox gene expression. , 2001, Development.

[85]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[86]  S. Poux,et al.  Structure of a Polycomb Response Element and In Vitro Binding of Polycomb Group Complexes Containing GAGA Factor , 2000, Molecular and Cellular Biology.

[87]  Mark J Alkema,et al.  Genetic interactions and dosage effects of Polycomb group genes in mice. , 1998, Development.

[88]  P. Schedl,et al.  A Polycomb and GAGA dependent silencer adjoins the Fab-7 boundary in the Drosophila bithorax complex. , 1997, Genetics.

[89]  M. Sofroniew,et al.  Posterior transformation, neurological abnormalities, and severe hematopoietic defects in mice with a targeted deletion of the bmi-1 proto-oncogene. , 1994, Genes & development.

[90]  Judith K. Brown,et al.  Polycomb group response elements in Drosophila and vertebrates. , 2013, Advances in genetics.

[91]  Vincenzo Pirrotta,et al.  Polycomb silencing mechanisms and the management of genomic programmes , 2007, Nature Reviews Genetics.