Raf1 Is a DCAF for the Rik1 DDB1-Like Protein and Has Separable Roles in siRNA Generation and Chromatin Modification
Non-coding transcription can trigger histone post-translational modifications forming specialized chromatin. In fission yeast, heterochromatin formation requires RNAi and the histone H3K9 methyltransferase complex CLRC, composed of Clr4, Raf1, Raf2, Cul4, and Rik1. CLRC mediates H3K9 methylation and siRNA production; it also displays E3-ubiquitin ligase activity in vitro. DCAFs act as substrate receptors for E3 ligases and may couple ubiquitination with histone methylation. Here, structural alignment and mutation of signature WDxR motifs in Raf1 indicate that it is a DCAF for CLRC. We demonstrate that Raf1 promotes H3K9 methylation and siRNA amplification via two distinct, separable functions. The association of the DCAF Raf1 with Cul4-Rik1 is critical for H3K9 methylation, but dispensable for processing of centromeric transcripts into siRNAs. Thus the association of a DCAF, Raf1, with its adaptor, Rik1, is required for histone methylation and to allow RNAi to signal to chromatin.
Vyšlo v časopise:
Raf1 Is a DCAF for the Rik1 DDB1-Like Protein and Has Separable Roles in siRNA Generation and Chromatin Modification. PLoS Genet 8(2): e32767. doi:10.1371/journal.pgen.1002499
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002499
Souhrn
Non-coding transcription can trigger histone post-translational modifications forming specialized chromatin. In fission yeast, heterochromatin formation requires RNAi and the histone H3K9 methyltransferase complex CLRC, composed of Clr4, Raf1, Raf2, Cul4, and Rik1. CLRC mediates H3K9 methylation and siRNA production; it also displays E3-ubiquitin ligase activity in vitro. DCAFs act as substrate receptors for E3 ligases and may couple ubiquitination with histone methylation. Here, structural alignment and mutation of signature WDxR motifs in Raf1 indicate that it is a DCAF for CLRC. We demonstrate that Raf1 promotes H3K9 methylation and siRNA amplification via two distinct, separable functions. The association of the DCAF Raf1 with Cul4-Rik1 is critical for H3K9 methylation, but dispensable for processing of centromeric transcripts into siRNAs. Thus the association of a DCAF, Raf1, with its adaptor, Rik1, is required for histone methylation and to allow RNAi to signal to chromatin.
Zdroje
1. FaraziTAJuranekSATuschlT 2008 The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135 1201 1214
2. GrewalSI 2010 RNAi-dependent formation of heterochromatin and its diverse functions. Curr Opin Genet Dev 20 134 141
3. MoazedD 2009 Small RNAs in transcriptional gene silencing and genome defence. Nature 457 413 420
4. GuangSBochnerAFBurkhartKBBurtonNPavelecDM 2010 Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature 465 1097 1101
5. Kuramochi-MiyagawaSWatanabeTGotohKTotokiYToyodaA 2008 DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev 22 908 917
6. AllshireRCJaverzatJPRedheadNJCranstonG 1994 Position effect variegation at fission yeast centromeres. Cell 76 157 169
7. DjupedalIPortosoMSpahrHBonillaCGustafssonCM 2005 RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev 19 2301 2306
8. KatoHGotoDBMartienssenRAUranoTFurukawaK 2005 RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309 467 469
9. VolpeTAKidnerCHallIMTengGGrewalSI 2002 Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297 1833 1837
10. BayneEHWhiteSAKaganskyABijosDASanchez-PulidoL 2010 Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell 140 666 677
11. SadaieMIidaTUranoTNakayamaJ 2004 A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. Embo J 23 3825 3835
12. BannisterAJZegermanPPartridgeJFMiskaEAThomasJO 2001 Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410 120 124
13. ZhangKMoschKFischleWGrewalSI 2008 Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat Struct Mol Biol 15 381 388
14. PetrieVJWuitschickJDGivensCDKosinskiAMPartridgeJF 2005 RNA interference (RNAi)-dependent and RNAi-independent association of the Chp1 chromodomain protein with distinct heterochromatic loci in fission yeast. Mol Cell Biol 25 2331 2346
15. SugiyamaTCamHPSugiyamaRNomaKZofallM 2007 SHREC, an effector complex for heterochromatic transcriptional silencing. Cell 128 491 504
16. BuhlerMVerdelAMoazedD 2006 Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125 873 886
17. 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
18. MotamediMRVerdelAColmenaresSUGerberSAGygiSP 2004 Two RNAi complexes, RITS and RDRC, physically interact and localise to noncoding centromeric RNAs. Cell 119 789 802
19. NomaKSugiyamaTCamHVerdelAZofallM 2004 RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat Genet 36 1174 1180
20. DjupedalIKos-BraunICMosherRASoderholmNSimmerF 2009 Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. EMBO J 28 3832 3844
21. GeraceELHalicMMoazedD 2010 The methyltransferase activity of Clr4Suv39h triggers RNAi independently of histone H3K9 methylation. Mol Cell 39 360 372
22. JiaSKobayashiRGrewalSI 2005 Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat Cell Biol 7 1007 1013
23. LiFGotoDBZaratieguiMTangXMartienssenR 2005 Two novel proteins, dos1 and dos2, interact with rik1 to regulate heterochromatic RNA interference and histone modification. Curr Biol 15 1448 1457
24. HornPJBastieJNPetersonCL 2005 A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev 19 1705 1714
25. ThonGHansenKRAltesSPSidhuDSinghG 2005 The Clr7 and Clr8 directionality factors and the Pcu4 cullin mediate heterochromatin formation in the fission yeast Schizosaccharomyces pombe. Genetics 171 1583 1595
26. JacksonSXiongY 2009 CRL4s: the CUL4-RING E3 ubiquitin ligases. Trends Biochem Sci 34 562 570
27. ShilatifardA 2006 Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem 75 243 269
28. PetroskiMDDeshaiesRJ 2005 Function and regulation of cullin-RING ubiquitin ligases. Nat Rev Mol Cell Biol 6 9 20
29. KapetanakiMGGuerrero-SantoroJBisiDCHsiehCLRapic-OtrinV 2006 The DDB1-CUL4ADDB2 ubiquitin ligase is deficient in xeroderma pigmentosum group E and targets histone H2A at UV-damaged DNA sites. Proc Natl Acad Sci U S A 103 2588 2593
30. WangHZhaiLXuJJooHYJacksonS 2006 Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage. Mol Cell 22 383 394
31. HigaLAWuMYeTKobayashiRSunH 2006 CUL4-DDB1 ubiquitin ligase interacts with multiple WD-40-repeat proteins and regulates histone methylation. Nat Cell Biol 8 1277 1283
32. JinJAriasEEChenJHarperJWWalterJC 2006 A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which is required for S phase destruction of the replication factor Cdt1. Mol Cell 23 709 721
33. AngersSLiTYiXMacCossMJMoonRT 2006 Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature 443 590 593
34. HeYJMcCallCMHuJZengYXiongY 2006 DDB1 functions as a linker to recruit receptor WD-40 proteins to CUL4-ROC1 ubiquitin ligases. Genes Dev 20 2949 2954
35. LiuCPowellKAMundtKWuLCarrAM 2003 Cop9/signalosome subunits and Pcu4 regulate ribonucleotide reductase by both checkpoint-dependent and -independent mechanisms. Genes Dev 17 1130 1140
36. NeuwaldAFPoleksicA 2000 PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. Nucleic Acids Res 28 3570 3580
37. BraunSGarciaJFRowleyMRougemailleMShankarS 2011 The cul4-ddb1(cdt2) ubiquitin ligase inhibits invasion of a boundary-associated antisilencing factor into heterochromatin. Cell 144 41 54
38. PidouxALUzawaSPerryPECandeWZAllshireRC 2000 Live analysis of lagging chromosomes during anaphase and their effect on spindle elongation rate in fission yeast. J Cell Sci 113 Pt 23 4177 4191
39. LiFHuarteMZaratieguiMVaughnMWShiY 2008 Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin. Cell 135 272 283
40. BernardPMaureJFPartridgeJFGenierSJaverzatJP 2001 Requirement of heterochromatin for cohesion at centromeres. Science 294 2539 2542
41. NonakaNKitajimaTYokobayashiSXiaoGYamamotoM 2002 Recruitment of cohesin to heterochromatic regions by Swi6/HP1 in fission yeast. Nat Cell Biol 4 89 93
42. EkwallKJaverzatJPLorentzASchmidtHCranstonG 1995 The chromodomain protein Swi6: a key component at fission yeast centromeres. Science 269 1429 1431
43. HallIMShankaranarayanaGDNomaKAyoubNCohenA 2002 Establishment and maintenance of a heterochromatin domain. Science 297 2232 2237
44. ScrimaAKonickovaRCzyzewskiBKKawasakiYJeffreyPD 2008 Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex. Cell 135 1213 1223
45. HanZGuoLWangHShenYDengXW 2006 Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell 22 137 144
46. CoutureJFCollazoETrievelRC 2006 Molecular recognition of histone H3 by the WD-40 protein WDR5. Nat Struct Mol Biol 13 698 703
47. SchuetzAAllali-HassaniAMartinFLoppnauPVedadiM 2006 Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO J 25 4245 4252
48. ZhangKFischerTPorterRLDhakshnamoorthyJZofallM 2011 Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA. Science 331 1624 1627
49. LiFMartienssenRCandeWZ 2011 Coordination of DNA replication and histone modification by the Rik1-Dos2 complex. Nature 475 244 248
50. ChenESZhangKNicolasECamHPZofallM 2008 Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451 734 737
51. KlocAZaratieguiMNoraEMartienssenR 2008 RNA interference guides histone modification during the S phase of chromosomal replication. Curr Biol 18 490 495
52. KaganskyAFolcoHDAlmeidaRPidouxALBoukabaA 2009 Synthetic heterochromatin bypasses RNAi and centromeric repeats to establish functional centromeres. Science 324 1716 1719
53. MorenoSKlarANurseP 1991 Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol 194 795 823
54. PidouxAMelloneBAllshireR 2004 Analysis of chromatin in fission yeast. Methods 33 252 259
55. OeffingerMWeiKERogersRDeGrasseJAChaitBT 2007 Comprehensive analysis of diverse ribonucleoprotein complexes. Nat Methods 4 951 956
56. BayneEHPortosoMKaganskyAKos-BraunICUranoT 2008 Splicing factors facilitate RNAi-directed silencing in fission yeast. Science 322 602 606
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 2
- 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
- Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA
- Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in : Frequency, Effects, and Dominance
- Homeobox Genes Critically Regulate Embryo Implantation by Controlling Paracrine Signaling between Uterine Stroma and Epithelium
- Nondisjunction of a Single Chromosome Leads to Breakage and Activation of DNA Damage Checkpoint in G2