The PAF Complex and Prf1/Rtf1 Delineate Distinct Cdk9-Dependent Pathways Regulating Transcription Elongation in Fission Yeast

English version České info

Cyclin-dependent kinase 9 (Cdk9) promotes elongation by RNA polymerase II (RNAPII), mRNA processing, and co-transcriptional histone modification. Cdk9 phosphorylates multiple targets, including the conserved RNAPII elongation factor Spt5 and RNAPII itself, but how these different modifications mediate Cdk9 functions is not known. Here we describe two Cdk9-dependent pathways in the fission yeast Schizosaccharomyces pombe that involve distinct targets and elicit distinct biological outcomes. Phosphorylation of Spt5 by Cdk9 creates a direct binding site for Prf1/Rtf1, a transcription regulator with functional and physical links to the Polymerase Associated Factor (PAF) complex. PAF association with chromatin is also dependent on Cdk9 but involves alternate phosphoacceptor targets. Prf1 and PAF are biochemically separate in cell extracts, and genetic analyses show that Prf1 and PAF are functionally distinct and exert opposing effects on the RNAPII elongation complex. We propose that this opposition constitutes a Cdk9 auto-regulatory mechanism, such that a positive effect on elongation, driven by the PAF pathway, is kept in check by a negative effect of Prf1/Rtf1 and downstream mono-ubiquitylation of histone H2B. Thus, optimal RNAPII elongation may require balanced action of functionally distinct Cdk9 pathways.

Vyšlo v časopise: The PAF Complex and Prf1/Rtf1 Delineate Distinct Cdk9-Dependent Pathways Regulating Transcription Elongation in Fission Yeast. PLoS Genet 9(12): e32767. doi:10.1371/journal.pgen.1004029
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004029

Souhrn

Zdroje

1. ZhouQ, LiT, PriceDH (2012) RNA polymerase II elongation control. Annu Rev Biochem 81 : 119–143.

2. MarshallNF, PriceDH (1995) Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J Biol Chem 270 : 12335–12338.

3. WadaT, TakagiT, YamaguchiY, WatanabeD, HandaH (1998) Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro. Embo J 17 : 7395–7403.

4. YamadaT, YamaguchiY, InukaiN, OkamotoS, MuraT, et al. (2006) P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation. Mol Cell 21 : 227–237.

5. YamaguchiY, TakagiT, WadaT, YanoK, FuruyaA, et al. (1999) NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97 : 41–51.

6. MurrayS, UdupaR, YaoS, HartzogG, PrelichG (2001) Phosphorylation of the RNA polymerase II carboxy-terminal domain by the Bur1 cyclin-dependent kinase. Mol Cell Biol 21 : 4089–4096.

7. PeiY, DuH, SingerJ, St AmourC, GranittoS, et al. (2006) Cyclin-dependent kinase 9 (Cdk9) of fission yeast is activated by the CDK-activating kinase Csk1, overlaps functionally with the TFIIH-associated kinase Mcs6, and associates with the mRNA cap methyltransferase Pcm1 in vivo. Mol Cell Biol 26 : 777–788.

8. PeiY, SchwerB, ShumanS (2003) Interactions between fission yeast Cdk9, its cyclin partner Pch1, and mRNA capping enzyme Pct1 suggest an elongation checkpoint for mRNA quality control. J Biol Chem 278 : 7180–7188.

9. PeiY, ShumanS (2003) Characterization of the Schizosaccharomyces pombe Cdk9/Pch1 protein kinase: Spt5 phosphorylation, autophosphorylation, and mutational analysis. J Biol Chem 278 : 43346–43356.

10. KeoghMC, PodolnyV, BuratowskiS (2003) Bur1 kinase is required for efficient transcription elongation by RNA polymerase II. Mol Cell Biol 23 : 7005–7018.

11. SansoM, LeeKM, ViladevallL, JacquesPE, PageV, et al. (2012) A Positive Feedback Loop Links Opposing Functions of P-TEFb/Cdk9 and Histone H2B Ubiquitylation to Regulate Transcript Elongation in Fission Yeast. PLoS Genet 8: e1002822.

12. ViladevallL, St AmourCV, RosebrockA, SchneiderS, ZhangC, et al. (2009) TFIIH and P-TEFb coordinate transcription with capping enzyme recruitment at specific genes in fission yeast. Mol Cell 33 : 738–751.

13. PeterlinBM, PriceDH (2006) Controlling the elongation phase of transcription with P-TEFb. Mol Cell 23 : 297–305.

14. HsinJP, ManleyJL (2012) The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 26 : 2119–2137.

15. ZhouK, KuoWH, FillinghamJ, GreenblattJF (2009) Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5. Proc Natl Acad Sci U S A 106 : 6956–6961.

16. LiuY, WarfieldL, ZhangC, LuoJ, AllenJ, et al. (2009) Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol 29 : 4852–4863.

17. ShchebetA, KarpiukO, KremmerE, EickD, JohnsenSA (2012) Phosphorylation by cyclin-dependent kinase-9 controls ubiquitin-conjugating enzyme-2A function. Cell Cycle 11 : 2122–2127.

18. WoodA, SchneiderJ, DoverJ, JohnstonM, ShilatifardA (2005) The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS. Mol Cell 20 : 589–599.

19. SchneiderS, PeiY, ShumanS, SchwerB (2010) Separable functions of the fission yeast Spt5 carboxyl-terminal domain (CTD) in capping enzyme binding and transcription elongation overlap with those of the RNA polymerase II CTD. Mol Cell Biol 30 : 2353–2364.

20. TomsonBN, ArndtKM (2013) The many roles of the conserved eukaryotic Paf1 complex in regulating transcription, histone modifications, and disease states. Biochim Biophys Acta 1829 : 116–126.

21. ChenY, YamaguchiY, TsugenoY, YamamotoJ, YamadaT, et al. (2009) DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation. Genes Dev 23 : 2765–2777.

22. KimJ, GuermahM, RoederRG (2010) The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Cell 140 : 491–503.

23. RondonAG, GallardoM, Garcia-RubioM, AguileraA (2004) Molecular evidence indicating that the yeast PAF complex is required for transcription elongation. EMBO Rep 5 : 47–53.

24. PavriR, ZhuB, LiG, TrojerP, MandalS, et al. (2006) Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 125 : 703–717.

25. KroganNJ, DoverJ, WoodA, SchneiderJ, HeidtJ, et al. (2003) The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell 11 : 721–729.

26. ZhuB, MandalSS, PhamAD, ZhengY, Erdjument-BromageH, et al. (2005) The human PAF complex coordinates transcription with events downstream of RNA synthesis. Genes Dev 19 : 1668–1673.

27. PenheiterKL, WashburnTM, PorterSE, HoffmanMG, JaehningJA (2005) A posttranscriptional role for the yeast Paf1-RNA polymerase II complex is revealed by identification of primary targets. Mol Cell 20 : 213–223.

28. Rozenblatt-RosenO, NagaikeT, FrancisJM, KanekoS, GlattKA, et al. (2009) The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3′ mRNA processing factors. Proc Natl Acad Sci U S A 106 : 755–760.

29. LaribeeRN, KroganNJ, XiaoT, ShibataY, HughesTR, et al. (2005) BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Curr Biol 15 : 1487–1493.

30. QiuH, HuC, GaurNA, HinnebuschAG (2012) Pol II CTD kinases Bur1 and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex. Embo J 31 : 3494–3505.

31. MayekarMK, GardnerRG, ArndtKM (2013) The recruitment of the Saccharomyces cerevisiae Paf1 complex to active genes requires a domain of Rtf1 that directly interacts with the Spt4-Spt5 complex. Mol Cell Biol 33 : 3259–3273.

32. NordickK, HoffmanMG, BetzJL, JaehningJA (2008) Direct interactions between the Paf1 complex and a cleavage and polyadenylation factor are revealed by dissociation of Paf1 from RNA polymerase II. Eukaryot Cell 7 : 1158–1167.

33. AdelmanK, WeiW, ArdehaliMB, WernerJ, ZhuB, et al. (2006) Drosophila Paf1 modulates chromatin structure at actively transcribed genes. Mol Cell Biol 26 : 250–260.

34. LangenbacherAD, NguyenCT, CavanaughAM, HuangJ, LuF, et al. (2011) The PAF1 complex differentially regulates cardiomyocyte specification. Dev Biol 353 : 19–28.

35. Rozenblatt-RosenO, HughesCM, NannepagaSJ, ShanmugamKS, CopelandTD, et al. (2005) The parafibromin tumor suppressor protein is part of a human Paf1 complex. Mol Cell Biol 25 : 612–620.

36. KroganNJ, KimM, AhnSH, ZhongG, KoborMS, et al. (2002) RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol 22 : 6979–6992.

37. MuellerCL, JaehningJA (2002) Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol Cell Biol 22 : 1971–1980.

38. AkanumaT, KoshidaS, KawamuraA, KishimotoY, TakadaS (2007) Paf1 complex homologues are required for Notch-regulated transcription during somite segmentation. EMBO Rep 8 : 858–863.

39. BaiX, KimJ, YangZ, JurynecMJ, AkieTE, et al. (2010) TIF1gamma controls erythroid cell fate by regulating transcription elongation. Cell 142 : 133–143.

40. HeY, DoyleMR, AmasinoRM (2004) PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes Dev 18 : 2774–2784.

41. DingL, Paszkowski-RogaczM, NitzscheA, SlabickiMM, HeningerAK, et al. (2009) A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell 4 : 403–415.

42. BetzJL, ChangM, WashburnTM, PorterSE, MuellerCL, et al. (2002) Phenotypic analysis of Paf1/RNA polymerase II complex mutations reveals connections to cell cycle regulation, protein synthesis, and lipid and nucleic acid metabolism. Mol Genet Genomics 268 : 272–285.

43. ChuY, SimicR, WarnerMH, ArndtKM, PrelichG (2007) Regulation of histone modification and cryptic transcription by the Bur1 and Paf1 complexes. Embo J 26 : 4646–4656.

44. KeoghMC, KurdistaniSK, MorrisSA, AhnSH, PodolnyV, et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123 : 593–605.

45. LenstraTL, BenschopJJ, KimT, SchulzeJM, BrabersNA, et al. (2011) The specificity and topology of chromatin interaction pathways in yeast. Mol Cell 42 : 536–549.

46. PiroAS, MayekarMK, WarnerMH, DavisCP, ArndtKM (2012) Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast. Proc Natl Acad Sci U S A 109 : 10837–10842.

47. EydmannT, SommarivaE, InagawaT, MianS, KlarAJ, et al. (2008) Rtf1-mediated eukaryotic site-specific replication termination. Genetics 180 : 27–39.

48. RacineA, PageV, NagyS, GrabowskiD, TannyJC (2012) Histone H2B ubiquitylation promotes activity of the intact Set1 histone methyltransferase complex in fission yeast. J Biol Chem 287 : 19040–19047.

49. TannyJC, Erdjument-BromageH, TempstP, AllisCD (2007) Ubiquitylation of histone H2B controls RNA polymerase II transcription elongation independently of histone H3 methylation. Genes Dev 21 : 835–847.

50. ChandrasekharanMB, HuangF, SunZW (2010) Histone H2B ubiquitination and beyond: Regulation of nucleosome stability, chromatin dynamics and the trans-histone H3 methylation. Epigenetics 5 : 460–468.

51. St AmourCV, SansoM, BoskenCA, LeeKM, LarochelleS, et al. (2012) Separate domains of fission yeast Cdk9 (P-TEFb) are required for capping enzyme recruitment and primed (Ser7-phosphorylated) CTD substrate recognition. Mol Cell Biol 32 : 2372–2383.

52. PhatnaniHP, JonesJC, GreenleafAL (2004) Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome. Biochemistry 43 : 15702–15719.

53. SchwerB, ShumanS (2011) Deciphering the RNA polymerase II CTD code in fission yeast. Mol Cell 43 : 311–318.

54. WierAD, MayekarMK, HerouxA, ArndtKM, VandemarkAP (2013) Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Proc Natl Acad Sci U S A 110 : 17290–17295.

55. WarnerMH, RoinickKL, ArndtKM (2007) Rtf1 is a multifunctional component of the Paf1 complex that regulates gene expression by directing cotranscriptional histone modification. Mol Cell Biol 27 : 6103–6115.

56. MuellerCL, PorterSE, HoffmanMG, JaehningJA (2004) The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol Cell 14 : 447–456.

57. LindstromDL, HartzogGA (2001) Genetic interactions of Spt4-Spt5 and TFIIS with the RNA polymerase II CTD and CTD modifying enzymes in Saccharomyces cerevisiae. Genetics 159 : 487–497.

58. FlemingAB, KaoCF, HillyerC, PikaartM, OsleyMA (2008) H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation. Mol Cell 31 : 57–66.

59. ChandrasekharanMB, HuangF, SunZW (2009) Ubiquitination of histone H2B regulates chromatin dynamics by enhancing nucleosome stability. Proc Natl Acad Sci U S A 106 : 16686–16691.

60. BattaK, ZhangZ, YenK, GoffmanDB, PughBF (2011) Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes Dev 25 : 2254–2265.

61. WeinbergerL, VoichekY, TiroshI, HornungG, AmitI, et al. (2012) Expression Noise and Acetylation Profiles Distinguish HDAC Functions. Mol Cell 47 : 193–202.

62. ShemaE, KimJ, RoederRG, OrenM (2011) RNF20 Inhibits TFIIS-Facilitated Transcriptional Elongation to Suppress Pro-oncogenic Gene Expression. Mol Cell 42 : 477–488.

63. FujinagaK, IrwinD, HuangY, TaubeR, KurosuT, et al. (2004) Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element. Mol Cell Biol 24 : 787–795.

64. TastoJJ, CarnahanRH, McDonaldWH, GouldKL (2001) Vectors and gene targeting modules for tandem affinity purification in Schizosaccharomyces pombe. Yeast 18 : 657–662.

65. MorenoS, KlarA, NurseP (1991) Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol 194 : 795–823.

66. GuiguenA, SoutourinaJ, DewezM, TafforeauL, DieuM, et al. (2007) Recruitment of P-TEFb (Cdk9-Pch1) to chromatin by the cap-methyl transferase Pcm1 in fission yeast. EMBO J 26 : 1552–1559.