Insulators Target Active Genes to Transcription Factories and Polycomb-Repressed Genes to Polycomb Bodies
Polycomb bodies are foci of Polycomb proteins in which different Polycomb target genes are thought to co-localize in the nucleus, looping out from their chromosomal context. We have shown previously that insulators, not Polycomb response elements (PREs), mediate associations among Polycomb Group (PcG) targets to form Polycomb bodies. Here we use live imaging and 3C interactions to show that transgenes containing PREs and endogenous PcG-regulated genes are targeted by insulator proteins to different nuclear structures depending on their state of activity. When two genes are repressed, they co-localize in Polycomb bodies. When both are active, they are targeted to transcription factories in a fashion dependent on Trithorax and enhancer specificity as well as the insulator protein CTCF. In the absence of CTCF, assembly of Polycomb bodies is essentially reduced to those representing genomic clusters of Polycomb target genes. The critical role of Trithorax suggests that stable association with a specialized transcription factory underlies the cellular memory of the active state.
Vyšlo v časopise:
Insulators Target Active Genes to Transcription Factories and Polycomb-Repressed Genes to Polycomb Bodies. PLoS Genet 9(4): e32767. doi:10.1371/journal.pgen.1003436
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003436
Souhrn
Polycomb bodies are foci of Polycomb proteins in which different Polycomb target genes are thought to co-localize in the nucleus, looping out from their chromosomal context. We have shown previously that insulators, not Polycomb response elements (PREs), mediate associations among Polycomb Group (PcG) targets to form Polycomb bodies. Here we use live imaging and 3C interactions to show that transgenes containing PREs and endogenous PcG-regulated genes are targeted by insulator proteins to different nuclear structures depending on their state of activity. When two genes are repressed, they co-localize in Polycomb bodies. When both are active, they are targeted to transcription factories in a fashion dependent on Trithorax and enhancer specificity as well as the insulator protein CTCF. In the absence of CTCF, assembly of Polycomb bodies is essentially reduced to those representing genomic clusters of Polycomb target genes. The critical role of Trithorax suggests that stable association with a specialized transcription factory underlies the cellular memory of the active state.
Zdroje
1. ChakalovaL, DebrandE, MitchellJA, OsborneCS, FraserP (2005) Replication and transcription: shaping the landscape of the genome. Nat Rev Genet 6: 669–677 doi:10.1038/nrg1673.
2. MelnikS, DengB, PapantonisA, BabooS, CarrIM, et al. (2011) The proteomes of transcription factories containing RNA polymerases I, II or III. Nature methods 8: 963–968 doi:10.1038/nmeth.1705.
3. BantigniesF, GrimaudC, LavrovS, GabutM, CavalliG (2003) Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev 17: 2406–2420 doi:10.1101/gad.269503.
4. GrimaudC, BantigniesF, Pal-BhadraM, GhanaP, BhadraU, et al. (2006) RNAi components are required for nuclear clustering of Polycomb group response elements. Cell 124: 957–971 doi:10.1016/j.cell.2006.01.036.
5. PhillipsJE, CorcesVG (2009) CTCF: master weaver of the genome. Cell 137: 1194–1211 doi:10.1016/j.cell.2009.06.001.
6. KrivegaM, DeanA (2011) Insulators organize chromatin: emerging rules of the game. Mol Cell 44: 1–2 doi:10.1016/j.molcel.2011.09.009.
7. KimTH, AbdullaevZK, SmithAD, ChingKA, LoukinovDI, et al. (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128: 1231–1245 doi:10.1016/j.cell.2006.12.048.
8. BusheyAM, RamosE, CorcesVG (2009) Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev 23: 1338–1350 doi:10.1101/gad.1798209.
9. RoyS, ErnstJ, KharchenkoPV, KheradpourP, NegreN, et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787–1797 doi:10.1126/science.1198374.
10. TolhuisB, BlomM, KerkhovenRM, PagieL, TeunissenH, et al. (2011) Interactions among Polycomb Domains Are Guided by Chromosome Architecture. PLoS Genet 7: e1001343 doi:10.1371/journal.pgen.1001343.
11. SextonT, YaffeE, KenigsbergE, BantigniesF, LeblancB, et al. (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148: 458–472 doi:10.1016/j.cell.2012.01.010.
12. BantigniesF, RoureV, CometI, LeblancB, SchuettengruberB, et al. (2011) Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144: 214–226 doi:10.1016/j.cell.2010.12.026.
13. HagstromK, MullerM, SchedlP (1996) Fab-7 functions as a chromatin domain boundary to ensure proper segment specification by the Drosophila bithorax complex. Genes Dev 10: 3202–3215 doi:10.1101/gad.10.24.3202.
14. BusturiaA, LloydA, BejaranoF, ZavortinkM, XinH, et al. (2001) The MCP silencer of the Drosophila Abd-B gene requires both Pleiohomeotic and GAGA factor for the maintenance of repression. Development 128: 2163–2173.
15. GruzdevaN, KyrchanovaO, ParshikovA, KullyevA, GeorgievP (2005) The Mcp element from the bithorax complex contains an insulator that is capable of pairwise interactions and can facilitate enhancer-promoter communication. Mol Cell Biol 25: 3682–3689 doi:10.1128/MCB.25.9.3682-3689.2005.
16. KyrchanovaO, ToshchakovS, ParshikovA, GeorgievP (2007) Study of the functional interaction between Mcp insulators from the Drosophila bithorax complex: effects of insulator pairing on enhancer-promoter communication. Mol Cell Biol 27: 3035–3043 doi:10.1128/MCB.02203-06.
17. LiH-B, MüllerM, BahecharIA, KyrchanovaO, OhnoK, et al. (2011) Insulators, Not Polycomb Response Elements, Are Required for Long-Range Interactions between Polycomb Targets in. Mol Cell Biol 31: 616–625 doi:10.1128/MCB.00849-10.
18. VazquezJ, MüllerM, PirrottaV, SedatJW (2006) The Mcp element mediates stable long-range chromosome-chromosome interactions in Drosophila. Mol Biol Cell 17: 2158–2165 doi:10.1091/mbc.E06-01-0049.
19. HolohanEE, KwongC, AdryanB, BartkuhnM, HeroldM, et al. (2007) CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex. PLoS Genet 3: e112 doi:10.1371/journal.pgen.0030112.
20. MohanM, BartkuhnM, HeroldM, PhilippenA, HeinlN, et al. (2007) The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning. EMBO J 26: 4203–4214 doi:10.1038/sj.emboj.7601851.
21. LeiEP, CorcesVG (2006) RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 38: 936–941 doi:10.1038/ng1850.
22. MoshkovichN, NishaP, BoylePJ, ThompsonBa, DaleRK, et al. (2011) RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev 25: 1686–1701 doi:10.1101/gad.16651211.
23. WendtKS, YoshidaK, ItohT, BandoM, KochB, et al. (2008) Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451: 796–801 doi:10.1038/nature06634.
24. ParelhoV, HadjurS, SpivakovM, LeleuM, SauerS, et al. (2008) Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132: 422–433 doi:10.1016/j.cell.2008.01.011.
25. SchwartzYB, KahnTG, StenbergP, OhnoK, BourgonR, et al. (2010) Alternative epigenetic chromatin states of polycomb target genes. PLoS Genet 6: e1000805 doi:10.1371/journal.pgen.1000805.
26. CzerminB, MelfiR, McCabeD, SeitzV, ImhofA, et al. (2002) Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111: 185–196 doi:10.1016/S0092-8674(02)00975-3.
27. MilneTA, BriggsSD, BrockHW, MartinME, GibbsD, et al. (2002) MLL Targets SET Domain Methyltransferase Activity to Hox Gene Promoters. Mol Cell 10: 1107–1117 doi:10.1016/S1097-2765(02)00741-4.
28. NakamuraT, MoriT, TadaS, KrajewskiW, RozovskaiaT, et al. (2002) ALL-1 Is a Histone Methyltransferase that Assembles a Supercomplex of Proteins Involved in Transcriptional Regulation. Mol Cell 10: 1119–1128 doi:10.1016/S1097-2765(02)00740-2.
29. PouxS, HorardBB, SigristCJA, PirrottaV (2002) The Drosophila trithorax protein is a coactivator required to prevent re-establishment of polycomb silencing. Development 129: 2483–2493.
30. KlymenkoT, MüllerJ (2004) The histone methyltransferases Trithorax and Ash1 prevent transcriptional silencing by Polycomb group proteins. EMBO Rep 5: 373–377 doi:10.1038/sj.embor.7400111.
31. PouxS, KosticC, PirrottaV (1996) Hunchback-independent silencing of late Ubx enhancers by a Polycomb Group Response Element. EMBO J 15: 4713–4722.
32. MullerM, HagstromK, GyurkovicsH, PirrottaV, SchedlP (1999) The Mcp Element From the Drosophila melanogaster Bithorax Complex Mediates Long-Distance Regulatory Interactions. Genetics 153: 1333–1356.
33. PirrottaV, LiH-B (2012) A view of nuclear Polycomb bodies. Curr Opin Genet Dev 22: 101–109 doi:10.1016/j.gde.2011.11.004.
34. SigristCJ, PirrottaV (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.
35. SchwartzYB, Linder-BassoD, KharchenkoPV, TolstorukovMY, KimM, et al. (2012) Nature and function of insulator protein binding sites in the Drosophila genome. Genome research gr.138156.112–.
36. BowersSR, MirabellaF, Calero-NietoFJ, ValeauxS, HadjurS, et al. (2009) A conserved insulator that recruits CTCF and cohesin exists between the closely related but divergently regulated interleukin-3 and granulocyte-macrophage colony-stimulating factor genes. Mol Cell Biol 29: 1682–1693 doi:10.1128/MCB.01411-08.
37. KassisJA (2002) Pairing-sensitive silencing, polycomb group response elements, and transposon homing in Drosophila. Adv Genet 46: 421–438.
38. BlobelGA, KadaukeS, WangE, LauAW, ZuberJ, et al. (2009) A reconfigured pattern of MLL occupancy within mitotic chromatin promotes rapid transcriptional reactivation following mitotic exit. Mol Cell 36: 970–983 doi:10.1016/j.molcel.2009.12.001.
39. KageyMH, MelhuishTa, WottonD (2003) The polycomb protein Pc2 is a SUMO E3. Cell 113: 127–137.
40. MacPhersonMJ, BeattyLG, ZhouW, DuM, SadowskiPD (2009) The CTCF insulator protein is posttranslationally modified by SUMO. Mol Cell Biol 29: 714–725 doi:10.1128/MCB.00825-08.
41. GoldsboroughaS, KornbergTB (1996) Reduction of transcription by homologue asynapsis in Drosophila imaginal discs. Nature 381: 807–810 doi:10.1038/381807a0.
42. SpradlingA, RubinG (1982) Transposition of cloned P elements into Drosophila germ line chromosomes. Science 218: 341–347 doi:10.1126/science.6289435.
43. SiegalML, HartlDL (2000) Application of Cre/loxP in Drosophila. Site-specific recombination and transgene coplacement. Methods Mol Biol 136: 487–495 doi:10.1385/1-59259-065-9:487.
44. ThakarR, CsinkAK (2005) Changing chromatin dynamics and nuclear organization during differentiation in Drosophila larval tissue. J Cell Sci 118: 951–960 doi:10.1242/jcs.01684.
45. DekkerJ, RippeK, DekkerM, KlecknerN (2002) Capturing chromosome conformation. Science 295: 1306–1311 doi:10.1126/science.1067799.
46. HagègeH, KlousP, BraemC, SplinterE, DekkerJ, et al. (2007) Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc 2: 1722–1733 doi:10.1038/nprot.2007.243.
47. OhnoK, McCabeD, CzerminB, ImhofA, PirrottaV (2008) ESC, ESCL and their roles in Polycomb Group mechanisms. Mech Develop 125: 527–541 doi: 10.1016/mod.2008.01.002.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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