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Polycomb Bodies

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The Functional Nucleus

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Abstract

Polycomb bodies are concentrations of Polycomb Group proteins detectable in the nucleus at various intensities. The largest or most intense have been shown to contain genomic clusters of Polycomb Group targets such as the Hox gene clusters. Since, in general, the number of Polycomb bodies visible is an order of magnitude smaller than the known number of Polycomb target genes in the genome, they are often thought to involve the association of multiple genomic regions that are distant from one another in the genome. This chapter reviews the evidence for Polycomb bodies, their formation and their genomic content. While different lines of evidence indicate that genomically remote Polycomb target genes can associate, often enhancing the repressive effect, other evidence indicates that this is not usually a stable interaction, varies from one tissue to another, and is strongly dependent on the presence of insulator protein binding sites near Polycomb targets. The effects of transcriptional derepression and of post-transcriptional modifications of Polycomb proteins or of insulator proteins as factors modulating the association lf remote Polycomb target sites are also discussed.

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References

  • Aoki T, Schweinsberg S, Manasson J, Schedl P (2008) A stage-specific factor confers Fab-7 boundary activity during early embryogenesis in Drosophila. Mol Cell Biol 28(3):1047–1060

    Article  CAS  PubMed  Google Scholar 

  • Bantignies F, Grimaud C, Lavrov S, Gabut M, Cavalli G (2003) Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev 17:2406–2420

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bantignies F, Roure V, Comet I, Leblanc B, Schuettengruber B, Bonnet J, Tixier V, Mas A, Cavalli G (2011) Polycomb-dependent regulatory contacts between Distant Hox Loci in Drosophila. Cell 144(2):214–226

    Article  CAS  PubMed  Google Scholar 

  • Bernardi R, Pandolfi PP (2007) Structure, dynamics and functions of promyelocytic leukaemia nuclear bodies. Nat Rev Mol Cell Biol 8(12):1006–1016

    Article  CAS  PubMed  Google Scholar 

  • Bernstein E, Duncan EM, Masui O, Gil J, Heard E, Allis CD (2006) Mouse Polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol Cell Biol 26(7):2560–2569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buchenau P, Hodgson J, Strutt H, Arndt-Jovin DJ (1998) The distribution of polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing. J Cell Biol 141:469–481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chambeyron S, Da Silva NR, Lawson KA, Bickmore WA (2005) Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 132(9):2215–2223

    Article  CAS  PubMed  Google Scholar 

  • Cheutin T, Cavalli G (2012) Progressive Polycomb assembly on H3K27me3 compartments generates Polycomb bodies with developmentally regulated motion. PLoS Genet 8(1), e1002465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306–1311

    Article  CAS  PubMed  Google Scholar 

  • Deniaud E, Bickmore WA (2009) Transcription and the nuclear periphery: edge of darkness? Curr Opin Genet Dev 19(2):187–191

    Article  CAS  PubMed  Google Scholar 

  • Fedorova E, Sadoni N, Dahlsveen I, Koch J, Kremmer E, Eick D, Paro R, Zink D (2008) The nuclear organization of Polycomb/Trithorax group response elements in larval tissues of Drosophila melanogaster. Chromosome Res 16(4):649–673

    Article  CAS  PubMed  Google Scholar 

  • Ficz G, Heintzmann R, Arndt-Jovin DJ (2005) Polycomb group protein complexes exchange rapidly in living Drosophila. Development 132(17):3963–3976

    Article  CAS  PubMed  Google Scholar 

  • Gambetta MC, Oktaba K, Muller J (2009) Essential role of the glycosyltransferase Sxc/Ogt in Polycomb repression. Science 325(5936):93–96

    Article  CAS  PubMed  Google Scholar 

  • Gambetta MC, Müller J (2014) O-GlcNAcylation prevents aggregation of the Polycomb group repressor polyhomeotic. Dev Cell 31(5):629–639

    Article  CAS  PubMed  Google Scholar 

  • Gil J, Bernard D, Martinez D, Beach D (2004) Polycomb CBX7 has a unifying role in cellular lifespan. Nat Cell Biol 6:67–72

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez I, Mateos-Langerak J, Thomas A, Cheutin T, Cavalli G (2014) Identification of regulators of the three-dimensional Polycomb organization by a microscopy-based genome-wide RNAi screen. Mol Cell 54(3):485–499

    Article  CAS  PubMed  Google Scholar 

  • Grimaud C, Bantignies F, Pal-Bhadra M, Ghana P, Bhadra U, Cavalli G (2006) RNAi components are required for nuclear clustering of Polycomb group response elements. Cell 124:957–971

    Article  CAS  PubMed  Google Scholar 

  • Hernandez-Munoz I, Taghavi P, Kuijl C, Neefjes J, van Lohuizen M (2005) Association of BMI1 with Polycomb bodies is dynamic and requires PRC2/EZH2 and the maintenance DNA methyltransferase DNMT1. Mol Cell Biol 25(24):11047–11058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Isono K, Endo TA, Ku M, Yamada D, Suzuki R, Sharif J, Ishikura T, Toyoda T, Bernstein BE, Koseki H (2013) SAM Domain polymerization links subnuclear clustering of PRC1 to gene silencing. Dev Cell 26(6):565–577

    Article  CAS  PubMed  Google Scholar 

  • Kagey MH, Melhuish TA, Wotton D (2003) The Polycomb protein Pc2 is a SUMO E3. Cell 113:127–137

    Article  CAS  PubMed  Google Scholar 

  • Kim CA, Gingery M, Pilpa RM, Bowie JU (2002) The SAM domain of polyhomeotic forms a helical polymer. Nat Struct Biol 9:453–456

    CAS  PubMed  Google Scholar 

  • Klauke K, Radulovic V, Broekhuis M, Weersing E, Zwart E, Olthof S, Ritsema M, Bruggeman S, Wu X, Helin K, Bystrykh L, de Haan G (2013) Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation. Nat Cell Biol 15:353–362

    Article  CAS  PubMed  Google Scholar 

  • Kung JT, Kesner B, An JY, Ahn JY, Cifuentes-Rojas C, Colognori D, Jeon Y, Szanto A, del Rosario BC, Pinter SF, Erwin JA, Lee JT (2015) Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Mol Cell 57(2):361–375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lanzuolo C, Roure V, Dekker J, Bantignies F, Orlando V (2007) Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol 9(10):1167–1174

    Article  CAS  PubMed  Google Scholar 

  • Lei EP, Corces VG (2006) RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 38:936–941

    Article  CAS  PubMed  Google Scholar 

  • Li H-B, Muller M, Bahechar IA, Kyrchanova O, Ohno K, Georgiev P, Pirrotta V (2011) Insulators, not Polycomb response elements, are required for long-range interactions between Polycomb targets in Drosophila melanogaster. Mol Cell Biol 31(4):616–625

    Article  CAS  PubMed  Google Scholar 

  • Li H-B, Ohno K, Gui H, Pirrotta V (2013) Insulators target active genes to transcription factories and Polycomb-repressed genes to Polycomb bodies. PLoS Genet 9(4), e1003436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289–293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • MacPherson MJ, Beatty LG, Zhou W, Du M, Sadowski PD (2009) The CTCF insulator protein is posttranslationally modified by SUMO. Mol Cell Biol 29(3):714–725

    Article  CAS  PubMed  Google Scholar 

  • Mao YS, Zhang B, Spector DL (2011) Biogenesis and function of nuclear bodies. Trends Genet 27(8):295–306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morey C, Da Silva NR, Perry P, Bickmore WA (2007) Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development 134(5):909–919

    Article  CAS  PubMed  Google Scholar 

  • Morey L et al (2012) Nonoverlapping functions of the Polycomb Group Cbx family of proteins in embryonic stem cells. Cell Stem Cell 10(1):47–62

    Article  CAS  PubMed  Google Scholar 

  • Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK, Lei EP (2011) RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev 25(16):1686–1701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muller M, Hagstrom K, Gyurkovics H, Pirrotta V, Schedl P (1999) The Mcp element from the Drosophila melanogaster bithorax complex mediates long-distance regulatory interactions. Genetics 153:1333–1356

    CAS  PubMed  PubMed Central  Google Scholar 

  • Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D (2011) The dynamic architecture of Hox gene clusters. Science 334(6053):222–225

    Article  CAS  PubMed  Google Scholar 

  • Noordermeer D, Leleu M, Schorderet P, Joye E, Chabaud F, Duboule D, Krumlauf R (2014) Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci. eLife 3, e02557

    Article  PubMed  PubMed Central  Google Scholar 

  • Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36:1065–1071

    Article  CAS  PubMed  Google Scholar 

  • Pirrotta V, Li H-B (2012) A view of nuclear Polycomb bodies. Curr Opin Genet Dev 22(2):101–109

    Article  CAS  PubMed  Google Scholar 

  • Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7):1665–1680

    Article  CAS  PubMed  Google Scholar 

  • Ren X, Vincenz C, Kerppola TK (2008) Changes in the distributions and dynamics of Polycomb repressive complexes during embryonic stem cell differentiation. Mol Cell Biol 28(9):2884–2895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robinson AK, Leal BZ, Chadwell LV, Wang R, Ilangovan U, Kaur Y, Junco SE, Schirf V, Osmulski PA, Gaczynska M, Hinck AP, Demeler B, McEwen DG, Kim CA (2012) The growth-suppressive function of the Polycomb group protein polyhomeotic is mediated by polymerization of its Sterile Alpha Motif (SAM) domain. J Biol Chem 287(12):8702–8713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saurin AJ, Shiels C, Williamson J, Satijn DPE, Otte AP, Sheer D, Freemont PS (1998) The human Polycomb Group complex associates with pericentromeric heterochromatin to form a novel nuclear domain. J Cell Biol 142:887–898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schwartz YB, Pirrotta V (2013) A new world of Polycombs: unexpected partnerships and emerging functions. Nat Rev Genet 14(12):853–864

    Article  CAS  PubMed  Google Scholar 

  • Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148(3):458–472

    Article  CAS  PubMed  Google Scholar 

  • Sigrist CJA, Pirrotta V (1997) Chromatin insulator elements block the silencing of a target gene by the Drosophila Polycomb Response Element (PRE) but allow trans interactions between PREs on different chromosomes. Genetics 147:209–221

    CAS  PubMed  PubMed Central  Google Scholar 

  • Simon JA, Kingston RE (2013) Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol Cell 49(5):808–824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348–1354

    Article  CAS  PubMed  Google Scholar 

  • Sinclair DAR, Syrzycka M, Macauley MS, Rastgardani T, Komljenovic I, Vocadlo DJ, Brock HW, Honda BM (2009) Drosophila O-GlcNAc transferase (OGT) is encoded by the Polycomb group (PcG) gene, super sex combs (sxc). Proc Natl Acad Sci U S A 106(32):13427–13432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tolhuis B, Blom M, Kerkhoven RM, Pagie L, Teunissen H, Nieuwland M, Simonis M, de Laat W, van Lohuizen M, van Steensel B (2011) Interactions among Polycomb domains are guided by chromosome architecture. PLoS Genet 7(3), e1001343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vatolina TY, Boldyreva LV, Demakova OV, Demakov SA, Kokoza EB, Semeshin VF, Babenko VN, Goncharov FP, Belyaeva ES, Zhimulev IF (2011) Identical functional organization of nonpolytene and polytene chromosomes in Drosophila melanogaster. PLoS One 6(10), e25960

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vazquez J, Müller M, Pirrotta V, Sedat JW (2006) The Mcp element mediates stable long-range chromosome-chromosome interactions in Drosophila. Mol Biol Cell 17:2158–2165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Voncken JW, Schweizer D, Aagaard L, Sattler L, Jantsch MF, van Lohuizen M (1999) Chromatin association of the Polycomb group protein BMI1 is cell cycle-regulated and correlates with it phosphorylation status. J Cell Sci 112:4627–4639

    CAS  PubMed  Google Scholar 

  • Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472(7341):120–124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Molecular Biology and Biochemistry, Rutgers University, Nelso Laboratories, 604 Allison Road, Piscataway, NJ, 08854, USA

    Vincenzo Pirrotta

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  1. Vincenzo Pirrotta
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Correspondence to Vincenzo Pirrotta .

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Editors and Affiliations

  1. Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada

    David P. Bazett-Jones

  2. Dalhousie University, Halifax, Nova Scotia, Canada

    Graham Dellaire

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Pirrotta, V. (2016). Polycomb Bodies. In: Bazett-Jones, D., Dellaire, G. (eds) The Functional Nucleus. Springer, Cham. https://doi.org/10.1007/978-3-319-38882-3_7

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