Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion
Polycomb group (PcG) proteins are conserved chromatin factors that maintain silencing of key developmental genes outside of their expression domains. Recent genome-wide analyses showed a Polycomb (PC) distribution with binding to discrete PcG response elements (PREs). Within the cell nucleus, PcG proteins localize in structures called PC bodies that contain PcG-silenced genes, and it has been recently shown that PREs form local and long-range spatial networks. Here, we studied the nuclear distribution of two PcG proteins, PC and Polyhomeotic (PH). Thanks to a combination of immunostaining, immuno-FISH, and live imaging of GFP fusion proteins, we could analyze the formation and the mobility of PC bodies during fly embryogenesis as well as compare their behavior to that of the condensed fraction of euchromatin. Immuno-FISH experiments show that PC bodies mainly correspond to 3D structural counterparts of the linear genomic domains identified in genome-wide studies. During early embryogenesis, PC and PH progressively accumulate within PC bodies, which form nuclear structures localized on distinct euchromatin domains containing histone H3 tri-methylated on K27. Time-lapse analysis indicates that two types of motion influence the displacement of PC bodies and chromatin domains containing H2Av-GFP. First, chromatin domains and PC bodies coordinately undergo long-range motions that may correspond to the movement of whole chromosome territories. Second, each PC body and chromatin domain has its own fast and highly constrained motion. In this motion regime, PC bodies move within volumes slightly larger than those of condensed chromatin domains. Moreover, both types of domains move within volumes much smaller than chromosome territories, strongly restricting their possibility of interaction with other nuclear structures. The fast motion of PC bodies and chromatin domains observed during early embryogenesis strongly decreases in late developmental stages, indicating a possible contribution of chromatin dynamics in the maintenance of stable gene silencing.
Vyšlo v časopise:
Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion. PLoS Genet 8(1): e32767. doi:10.1371/journal.pgen.1002465
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002465
Souhrn
Polycomb group (PcG) proteins are conserved chromatin factors that maintain silencing of key developmental genes outside of their expression domains. Recent genome-wide analyses showed a Polycomb (PC) distribution with binding to discrete PcG response elements (PREs). Within the cell nucleus, PcG proteins localize in structures called PC bodies that contain PcG-silenced genes, and it has been recently shown that PREs form local and long-range spatial networks. Here, we studied the nuclear distribution of two PcG proteins, PC and Polyhomeotic (PH). Thanks to a combination of immunostaining, immuno-FISH, and live imaging of GFP fusion proteins, we could analyze the formation and the mobility of PC bodies during fly embryogenesis as well as compare their behavior to that of the condensed fraction of euchromatin. Immuno-FISH experiments show that PC bodies mainly correspond to 3D structural counterparts of the linear genomic domains identified in genome-wide studies. During early embryogenesis, PC and PH progressively accumulate within PC bodies, which form nuclear structures localized on distinct euchromatin domains containing histone H3 tri-methylated on K27. Time-lapse analysis indicates that two types of motion influence the displacement of PC bodies and chromatin domains containing H2Av-GFP. First, chromatin domains and PC bodies coordinately undergo long-range motions that may correspond to the movement of whole chromosome territories. Second, each PC body and chromatin domain has its own fast and highly constrained motion. In this motion regime, PC bodies move within volumes slightly larger than those of condensed chromatin domains. Moreover, both types of domains move within volumes much smaller than chromosome territories, strongly restricting their possibility of interaction with other nuclear structures. The fast motion of PC bodies and chromatin domains observed during early embryogenesis strongly decreases in late developmental stages, indicating a possible contribution of chromatin dynamics in the maintenance of stable gene silencing.
Zdroje
1. JenuweinTAllisCD 2001 Translating the histone code. Science 293 1074 1080
2. ShaoZRaibleFMollaaghababaRGuyonJRWuCT 1999 Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell 98 37 46
3. SimonJAKingstonRE 2009 Mechanisms of Polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol
4. SchwartzYBPirrottaV 2007 Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8 9 22
5. SchuettengruberBChourroutDVervoortMLeblancBCavalliG 2007 Genome regulation by polycomb and trithorax proteins. Cell 128 735 745
6. NegreNHennetinJSunLVLavrovSBellisM 2006 Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol 4 e170 doi:10.1371/journal.pbio.0040170
7. SchuettengruberBGanapathiMLeblancBPortosoMJaschekR 2009 Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol 7 e13 doi:10.1371/journal.pbio.1000013
8. MullerJVerrijzerP 2009 Biochemical mechanisms of gene regulation by polycomb group protein complexes. Curr Opin Genet Dev 19 150 158
9. LanzuoloCRoureVDekkerJBantigniesFOrlandoV 2007 Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol 9 1167 1174
10. BantigniesFRoureVCometILeblancBSchuettengruberB 2011 Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144 214 226
11. TolhuisBBlomMKerkhovenRMPagieLTeunissenH 2011 Interactions among Polycomb Domains Are Guided by Chromosome Architecture. PLoS Genet 7 e1001343 doi:10.1371/journal.pgen.1001343
12. BantigniesFGrimaudCLavrovSGabutMCavalliG 2003 Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev 17 2406 2420
13. VazquezJMullerMPirrottaVSedatJW 2006 The Mcp element mediates stable long-range chromosome-chromosome interactions in Drosophila. Mol Biol Cell 17 2158 2165
14. LiHBMullerMBahecharIAKyrchanovaOOhnoK 2010 Insulators, not Polycomb Response Elements, are required for long-range interactions between Polycomb targets in Drosophila. Mol Cell Biol
15. GrimaudCBantigniesFPal-BhadraMGhanaPBhadraU 2006 RNAi components are required for nuclear clustering of Polycomb group response elements. Cell 124 957 971
16. BuchenauPHodgsonJStruttHArndt-JovinDJ 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
17. MessmerSFrankeAParoR 1992 Analysis of the functional role of the Polycomb chromo domain in Drosophila melanogaster. Genes Dev 6 1241 1254
18. EskelandRLeebMGrimesGRKressCBoyleS 2010 Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol Cell 38 452 464
19. TerranovaRYokobayashiSStadlerMBOtteAPvan LohuizenM 2008 Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell 15 668 679
20. FiczGHeintzmannRArndt-JovinDJ 2005 Polycomb group protein complexes exchange rapidly in living Drosophila. Development 132 3963 3976
21. RenXVincenzCKerppolaTK 2008 Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation. Mol Cell Biol 28 2884 2895
22. MarshallWFStraightAMarkoJFSwedlowJDernburgA 1997 Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 7 930 939
23. VazquezJBelmontASSedatJW 2001 Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr Biol 11 1227 1239
24. ChubbJRBoyleSPerryPBickmoreWA 2002 Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12 439 445
25. HeunPLarocheTShimadaKFurrerPGasserSM 2001 Chromosome dynamics in the yeast interphase nucleus. Science 294 2181 2186
26. ThakarRCsinkAK 2005 Changing chromatin dynamics and nuclear organization during differentiation in Drosophila larval tissue. J Cell Sci 118 951 960
27. ChuangCHCarpenterAEFuchsovaBJohnsonTde LanerolleP 2006 Long-range directional movement of an interphase chromosome site. Curr Biol 16 825 831
28. DundrMOspinaJKSungMHJohnSUpenderM 2007 Actin-dependent intranuclear repositioning of an active gene locus in vivo. J Cell Biol 179 1095 1103
29. PlataniMGoldbergILamondAISwedlowJR 2002 Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4 502 508
30. GorischSMWachsmuthMIttrichCBacherCPRippeK 2004 Nuclear body movement is determined by chromatin accessibility and dynamics. Proc Natl Acad Sci U S A 101 13221 13226
31. AlkemaMJBronkMVerhoevenEOtteAvan 't VeerLJ 1997 Identification of Bmi1-interacting proteins as constituents of a multimeric mammalian polycomb complex. Genes Dev 11 226 240
32. SaurinAJShielsCWilliamsonJSatijnDPOtteAP 1998 The human polycomb group complex associates with pericentromeric heterochromatin to form a novel nuclear domain. J Cell Biol 142 887 898
33. NetterSFaucheuxMTheodoreL 2001 Developmental dynamics of a polyhomeotic-EGFP fusion in vivo. DNA Cell Biol 20 483 492
34. DietzelSNiemannHBrucknerBMaurangeCParoR 1999 The nuclear distribution of Polycomb during Drosophila melanogaster development shown with a GFP fusion protein. Chromosoma 108 83 94
35. SchwartzYBKahnTGNixDALiXYBourgonR 2006 Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 38 700 705
36. TolhuisBde WitEMuijrersITeunissenHTalhoutW 2006 Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat Genet 38 694 699
37. ManakJRDikeSSementchenkoVKapranovPBiemarF 2006 Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet 38 1151 1158
38. KosmanDMizutaniCMLemonsDCoxWGMcGinnisW 2004 Multiplex detection of RNA expression in Drosophila embryos. Science 305 846
39. JaglaKJaglaTHeitzlerPDretzenGBellardF 1997 ladybird, a tandem of homeobox genes that maintain late wingless expression in terminal and dorsal epidermis of the Drosophila embryo. Development 124 91 100
40. RieckhofGECasaresFRyooHDAbu-ShaarMMannRS 1997 Nuclear translocation of extradenticle requires homothorax, which encodes an extradenticle-related homeodomain protein. Cell 91 171 183
41. KerberBFellertSHochM 1998 Seven-up, the Drosophila homolog of the COUP-TF orphan receptors, controls cell proliferation in the insect kidney. Genes & development 12 1781 1786
42. SwaminathanJBaxterEMCorcesVG 2005 The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin. Genes Dev 19 65 76
43. MavrichTNJiangCIoshikhesIPLiXVentersBJ 2008 Nucleosome organization in the Drosophila genome. Nature 453 358 362
44. LeachTJMazzeoMChotkowskiHLMadiganJPWotringMG 2000 Histone H2A.Z is widely but nonrandomly distributed in chromosomes of Drosophila melanogaster. J Biol Chem 275 23267 23272
45. CmarkoDVerschurePJOtteAPvan DrielRFakanS 2003 Polycomb group gene silencing proteins are concentrated in the perichromatin compartment of the mammalian nucleus. J Cell Sci 116 335 343
46. FrancisNJKingstonREWoodcockCL 2004 Chromatin compaction by a polycomb group protein complex. Science 306 1574 1577
47. MargueronRLiGSarmaKBlaisAZavadilJ 2008 Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol Cell 32 503 518
48. FitzgeraldDPBenderW 2001 Polycomb group repression reduces DNA accessibility. Mol Cell Biol 21 6585 6597
49. LeviVRuanQPlutzMBelmontASGrattonE 2005 Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope. Biophys J 89 4275 4285
50. SimonisMKlousPSplinterEMoshkinYWillemsenR 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38 1348 1354
51. WachsmuthMCaudron-HergerMRippeK 2008 Genome organization: balancing stability and plasticity. Biochim Biophys Acta 1783 2061 2079
52. CremerTCremerMDietzelSMullerSSoloveiI 2006 Chromosome territories–a functional nuclear landscape. Curr Opin Cell Biol 18 307 316
53. ThakarRGordonGCsinkAK 2006 Dynamics and anchoring of heterochromatic loci during development. J Cell Sci 119 4165 4175
54. MisteliT 2001 Protein dynamics: implications for nuclear architecture and gene expression. Science 291 843 847
55. FilionGJvan BemmelJGBraunschweigUTalhoutWKindJ 2010 Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143 212 224
56. LangevinJLe BorgneRRosenfeldFGhoMSchweisguthF 2005 Lethal giant larvae controls the localization of notch-signaling regulators numb, neuralized, and Sanpodo in Drosophila sensory-organ precursor cells. Curr Biol 15 955 962
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 1
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Poly(ADP-Ribose) Polymerase 1 (PARP-1) Regulates Ribosomal Biogenesis in Nucleoli
- Microenvironmental Regulation by Fibrillin-1
- Parallel Mapping and Simultaneous Sequencing Reveals Deletions in and Associated with Discrete Inherited Disorders in a Domestic Dog Breed
- Two-Component Elements Mediate Interactions between Cytokinin and Salicylic Acid in Plant Immunity