The SCF Ubiquitin E3 Ligase Ubiquitylates Sir4 and Functions in Transcriptional Silencing
In budding yeast, transcriptional silencing, which is important to regulate gene expression and maintain genome integrity, requires silent information regulator (Sir) proteins. In addition, Rtt106, a histone chaperone involved in nucleosome assembly, functions in transcriptional silencing. However, how transcriptional silencing is regulated during mitotic cell division is not well understood. We show that cells lacking Dia2, a component of the SCFDia2 E3 ubiquitin ligase involved in DNA replication, display defects in silencing at the telomere and HMR locus and that the F-box and C-terminal regions of Dia2, two regions important for Dia2's ubiquitylation activity, are required for proper transcriptional silencing at these loci. In addition, we show that Sir proteins are mislocalized in dia2Δ mutant cells. Mutations in Dia2 and Rtt106 result in a synergistic loss of silencing at the HMR locus and significant elevation of Sir4 proteins at the HMR locus, suggesting that silencing defects in dia2Δ mutant cells are due, at least in part, to the altered levels of Sir4 at silent chromatin. Supporting this idea, we show that SCFDia2 ubiquitylates Sir4 in vitro and in vivo. Furthermore, Sir4 binding to silent chromatin is dynamically regulated during the cell cycle, and this regulation is lost in dia2Δ mutant cells. These results demonstrate that the SCFDia2 complex is involved in transcriptional silencing, ubiquitylates Sir4, and regulates transcriptional silencing during the cell cycle.
Vyšlo v časopise:
The SCF Ubiquitin E3 Ligase Ubiquitylates Sir4 and Functions in Transcriptional Silencing. PLoS Genet 8(7): e32767. doi:10.1371/journal.pgen.1002846
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002846
Souhrn
In budding yeast, transcriptional silencing, which is important to regulate gene expression and maintain genome integrity, requires silent information regulator (Sir) proteins. In addition, Rtt106, a histone chaperone involved in nucleosome assembly, functions in transcriptional silencing. However, how transcriptional silencing is regulated during mitotic cell division is not well understood. We show that cells lacking Dia2, a component of the SCFDia2 E3 ubiquitin ligase involved in DNA replication, display defects in silencing at the telomere and HMR locus and that the F-box and C-terminal regions of Dia2, two regions important for Dia2's ubiquitylation activity, are required for proper transcriptional silencing at these loci. In addition, we show that Sir proteins are mislocalized in dia2Δ mutant cells. Mutations in Dia2 and Rtt106 result in a synergistic loss of silencing at the HMR locus and significant elevation of Sir4 proteins at the HMR locus, suggesting that silencing defects in dia2Δ mutant cells are due, at least in part, to the altered levels of Sir4 at silent chromatin. Supporting this idea, we show that SCFDia2 ubiquitylates Sir4 in vitro and in vivo. Furthermore, Sir4 binding to silent chromatin is dynamically regulated during the cell cycle, and this regulation is lost in dia2Δ mutant cells. These results demonstrate that the SCFDia2 complex is involved in transcriptional silencing, ubiquitylates Sir4, and regulates transcriptional silencing during the cell cycle.
Zdroje
1. GrothARochaWVerreaultAAlmouzniG 2007 Chromatin challenges during DNA replication and repair. Cell 128 721 733
2. ElginSCGrewalSI 2003 Heterochromatin: silence is golden. Curr Biol 13 R895 898
3. ProbstAVAlmouzniG 2008 Pericentric heterochromatin: dynamic organization during early development in mammals. Differentiation 76 15 23
4. GrunsteinM 1998 Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell 93 325 328
5. MoazedD 2001 Common themes in mechanisms of gene silencing. Mol Cell 8 489 498
6. RuscheLNKirchmaierALRineJ 2003 The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72 481 516
7. GrewalSIMoazedD 2003 Heterochromatin and epigenetic control of gene expression. Science 301 798 802
8. MoazedD 2011 Mechanisms for the inheritance of chromatin states. Cell 146 510 518
9. LiQBurgessRZhangZ 2012 All roads lead to chromatin: Multiple pathways for histone deposition. Biochim Biophys Acta 1819 238 246
10. TylerJKAdamsCRChenSRKobayashiRKamakakaRT 1999 The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402 555 560
11. HuangSZhouHTararaJZhangZ 2007 A novel role for histone chaperones CAF-1 and Rtt106p in heterochromatin silencing. Embo J 26 2274 2283
12. SharpJAFoutsETKrawitzDCKaufmanPD 2001 Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing. Curr Biol 11 463 473
13. HuangSZhouHKatzmannDHochstrasserMAtanasovaE 2005 Rtt106p is a histone chaperone involved in heterochromatin-mediated silencing. Proc Natl Acad Sci U S A 102 13410 13415
14. MorohashiHMaculinsTLabibK 2009 The amino-terminal TPR domain of Dia2 tethers SCF(Dia2) to the replisome progression complex. Curr Biol 19 1943 1949
15. BlakeDLukeBKanellisPJorgensenPGohT 2006 The F-box protein Dia2 overcomes replication impedance to promote genome stability in Saccharomyces cerevisiae. Genetics 174 1709 1727
16. KoeppDMKileACSwaminathanSRodriguez-RiveraV 2006 The F-box protein Dia2 regulates DNA replication. Mol Biol Cell 17 1540 1548
17. MimuraSKomataMKishiTShirahigeKKamuraT 2009 SCF(Dia2) regulates DNA replication forks during S-phase in budding yeast. Embo J 28 3693 3705
18. DeshaiesRJ 1999 SCF and Cullin/Ring H2-based ubiquitin ligases. Annu Rev Cell Dev Biol 15 435 467
19. KipreosETPaganoM 2000 The F-box protein family. Genome Biol 1 REVIEWS3002
20. TongAHBooneC 2006 Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol Biol 313 171 192
21. TongAHEvangelistaMParsonsABXuHBaderGD 2001 Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294 2364 2368
22. KaufmanPDKobayashiRStillmanB 1997 Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-I. Genes Dev 11 345 357
23. TrioloTSternglanzR 1996 Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. Nature 381 251 253
24. AparicioOMBillingtonBLGottschlingDE 1991 Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66 1279 1287
25. WangXConnellyJJWangCLSternglanzR 2004 Importance of the Sir3 N terminus and its acetylation for yeast transcriptional silencing. Genetics 168 547 551
26. AndressEJHolicREdelmannMJKesslerBMYuVP 2011 Dia2 controls transcription by mediating assembly of the RSC complex. PLoS One 6 e21172
27. KatayamaSKitamuraKLehmannANikaidoOTodaT 2002 Fission yeast F-box protein Pof3 is required for genome integrity and telomere function. Mol Biol Cell 13 211 224
28. Vega-PalasMAMartin-FigueroaEFlorencioFJ 2000 Telomeric silencing of a natural subtelomeric gene. Mol Gen Genet 263 287 291
29. LiQZhouHWurteleHDaviesBHorazdovskyB 2008 Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly. Cell 134 244 255
30. LingerJTylerJK 2005 The yeast histone chaperone chromatin assembly factor 1 protects against double-strand DNA-damaging agents. Genetics 171 1513 1522
31. HanJZhouHHorazdovskyBZhangKXuRM 2007 Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science 315 653 655
32. BurgessRJZhouHHanJZhangZ 2010 A role for Gcn5 in replication-coupled nucleosome assembly. Mol Cell 37 469 480
33. AiXParthunMR 2004 The nuclear Hat1p/Hat2p complex: a molecular link between type B histone acetyltransferases and chromatin assembly. Mol Cell 14 195 205
34. LiQFazlyAMZhouHHuangSZhangZ 2009 The elongator complex interacts with PCNA and modulates transcriptional silencing and sensitivity to DNA damage agents. PLoS Genet 5 e1000684
35. PalladinoFLarocheTGilsonEAxelrodAPillusL 1993 SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell 75 543 555
36. GottaMLarocheTFormentonAMailletLScherthanH 1996 The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J Cell Biol 134 1349 1363
37. HoppeGJTannyJCRudnerADGerberSADanaieS 2002 Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol Cell Biol 22 4167 4180
38. MarshallMMahoneyDRoseAHicksJBBroachJR 1987 Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Mol Cell Biol 7 4441 4452
39. CockellMPalladinoFLarocheTKyrionGLiuC 1995 The carboxy termini of Sir4 and Rap1 affect Sir3 localization: evidence for a multicomponent complex required for yeast telomeric silencing. J Cell Biol 129 909 924
40. LooSRineJ 1995 Silencing and heritable domains of gene expression. Annu Rev Cell Dev Biol 11 519 548
41. HanJLiQMcCulloughLKettelkampCFormosaT 2010 Ubiquitylation of FACT by the cullin-E3 ligase Rtt101 connects FACT to DNA replication. Genes Dev 24 1485 1490
42. HirotaTLippJJTohBHPetersJM 2005 Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin. Nature 438 1176 1180
43. FischleWTsengBSDormannHLUeberheideBMGarciaBA 2005 Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438 1116 1122
44. ChenESZhangKNicolasECamHPZofallM 2008 Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451 734 737
45. CollinsSRMillerKMMaasNLRoguevAFillinghamJ 2007 Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446 806 810
46. ZaidiIWRabutGPovedaAScheelHMalmstromJ 2008 Rtt101 and Mms1 in budding yeast form a CUL4(DDB1)-like ubiquitin ligase that promotes replication through damaged DNA. EMBO Rep 9 1034 1040
47. PanXYePYuanDSWangXBaderJS 2006 A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124 1069 1081
48. ZhangZShibaharaKStillmanB 2000 PCNA connects DNA replication to epigenetic inheritance in yeast. Nature 408 221 225
49. HongEJVillenJGeraceELGygiSPMoazedD 2005 A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol 2 106 111
50. HornPJBastieJNPetersonCL 2005 A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev 19 1705 1714
51. JiaSKobayashiRGrewalSI 2005 Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat Cell Biol 7 1007 1013
52. MimuraSYamaguchiTIshiiSNoroEKatsuraT 2010 Cul8/Rtt101 forms a variety of protein complexes that regulate DNA damage response and transcriptional silencing. J Biol Chem 285 9858 9867
53. HuangHKahanaAGottschlingDEPrakashLLiebmanSW 1997 The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae. Mol Cell Biol 17 6693 6699
54. SunZWAllisCD 2002 Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418 104 108
55. MoazedDJohnsonD 1996 A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell 86 667 677
56. KahanaAGottschlingDE 1999 DOT4 links silencing and cell growth in Saccharomyces cerevisiae. Mol Cell Biol 19 6608 6620
57. KahanaA 2001 The deubiquitinating enzyme Dot4p is involved in regulating nutrient uptake. Biochem Biophys Res Commun 282 916 920
58. DeshaiesRJJoazeiroCA 2009 RING domain E3 ubiquitin ligases. Annu Rev Biochem 78 399 434
59. FinleyD 2009 Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem 78 477 513
60. FinkbeinerMGSawanCOuzounovaMMurrRHercegZ 2008 HAT cofactor TRRAP mediates beta-catenin ubiquitination on the chromatin and the regulation of the canonical Wnt pathway. Cell Cycle 7 3908 3914
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 7
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