The Paf1 complex: Platform or player in RNA polymerase II transcription?

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1799, Issue 5-6, 2010, Pages 379-388

  Jaehning, Judith A ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

Histone modification; Paf1 complex; RNA 3' end formation; RNA polymerase II; Transcription elongation; Transcription termination

Indexed keywords

BETA CATENIN; BETA GALACTOSIDASE; HISTONE DEACETYLASE; HISTONE H2B; HISTONE H3; HISTONE H4; HOX PROTEIN; PAF1 COMPLEX; PEPTIDES AND PROTEINS; PROTEIN CDC73; PROTEIN CTR9; PROTEIN LEO1; PROTEIN PAF1; PROTEIN RTF1; RNA POLYMERASE II; TRANSCRIPTION ELONGATION FACTOR; TRANSCRIPTION FACTOR; TRANSLATION TERMINATION FACTOR; UNCLASSIFIED DRUG; CYCLIN DEPENDENT KINASE; DROSOPHILA PROTEIN; HISTONE; MESSENGER RNA; MULTIPROTEIN COMPLEX; NONHISTONE PROTEIN; NUCLEAR PROTEIN; PAF1 PROTEIN, DROSOPHILA; PAF1 PROTEIN, HUMAN; PAF1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; SGV1 PROTEIN, S CEREVISIAE; SPT5 TRANSCRIPTIONAL ELONGATION FACTOR;

ALLELE; BREAST CANCER; CARBOXY TERMINAL SEQUENCE; CARCINOGENESIS; CELL CYCLE PROGRESSION; CELL CYCLE REGULATION; CELL ELONGATION; CELL LINE; CELL PROLIFERATION; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME; CYTOPLASM; DEMETHYLATION; DOWN REGULATION; DROSOPHILA; EMBRYONIC STEM CELL; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE MUTATION; GENE SILENCING; GENETIC CODE; GENETIC TRANSCRIPTION; GROWTH RATE; GROWTH REGULATION; HISTONE ACETYLATION; HISTONE MODIFICATION; HISTONE UBIQUITINATION; HUMAN; HYPERPARATHYROIDISM; IMMUNOPRECIPITATION; JAW TUMOR; KIDNEY CANCER; NONHUMAN; OPEN READING FRAME; PANCREAS CANCER; PHENOTYPE; PLANT; POLYADENYLATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PURIFICATION; REVIEW; RNA CAPPING; RNA DEGRADATION; RNA TRANSCRIPTION; STEM CELL; STOMACH CANCER; TELOMERE; YEAST; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; GENETICS; METABOLISM;

EUKARYOTA;

ANIMALS; CHROMOSOMAL PROTEINS, NON-HISTONE; CYCLIN-DEPENDENT KINASES; DROSOPHILA PROTEINS; HISTONES; HUMANS; MODELS, BIOLOGICAL; MULTIPROTEIN COMPLEXES; NUCLEAR PROTEINS; RNA POLYMERASE II; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE PROTEINS; TELOMERE; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ELONGATION FACTORS;

EID: 77953277032     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2010.01.001     Document Type: Review

References (114)

1. P.A. Wade, W. Werel, R.C. Fentzke, N.E. Thompson, J.F. Leykam, R.R. Burgess, J.A. Jaehning, Z.F. Burton, A novel collection of accessory factors associated with yeast RNA polymerase II, Protein Expr. Purif. 8 (1996) 85-90.
2. Z.F. Burton, M. Killeen, M. Sopta, L.G. Ortolan, J. Greenblatt, RAP30/74: a general initiation factor that binds to RNA polymerase II,Mol.Cell. Biol. 8 (1988) 1602-1613.
3. Y.J. Kim, S. Bjorklund, Y. Li, M.H. Sayre, R.D. Kornberg, A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II, Cell 77 (1994) 599-608.
4. A.J. Koleske, R.A. Young, An RNA polymerase II holoenzyme responsive to activators, Nature 368 (1994) 466-469.
5. X. Shi, A. Finkelstein, A.J. Wolf, P.A. Wade, Z.F. Burton, J.A. Jaehning, Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription, Mol. Cell. Biol. 16 (1996) 669-676.
6. X. Shi, M. Chang, A.J.Wolf, C.H. Chang, A.A. Frazer-Abel, P.A.Wade, Z.F. Burton, J.A. Jaehning, Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme, Mol. Cell. Biol. 17 (1997) 1160-1169.
7. M. Chang, D. French-Cornay, H.Y. Fan, H. Klein, C.L. Denis, J.A. Jaehning, A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling, Mol. Cell. Biol. 19 (1999) 1056-1067.
8. S.E. Porter, T.M. Washburn, M. Chang, J.A. Jaehning, The yeast pafl-RNA polymerase II complex is required for full expression of a subset of cell cycleregulated genes, Eukaryot. Cell 1 (2002) 830-842.
9. C.L. Mueller, J.A. Jaehning, Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex, Mol. Cell. Biol. 22 (2002) 1971-1980.
10. S.L. Squazzo, P.J.Costa,D.L. Lindstrom, K.E. Kumer, R. Simic, J.L. Jennings,A.J. Link, K.M. Arndt, G.A. Hartzog, The Paf1 complex physically and functionally associates with transcription elongation factors in vivo, EMBO J. 21 (2002) 1764-1774.
11. N.J. Krogan,M. Kim, S.H. Ahn,G. Zhong,M.S. Kobor,G. Cagney, A. Emili, A. Shilatifard, S. Buratowski, J.F.Greenblatt, RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach, Mol. Cell. Biol. 22 (2002) 6979-6992.
12. L.A. Stolinski, D.M. Eisenmann, K.M. Arndt, Identification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae, Mol. Cell. Biol. 17 (1997) 4490-4500.
13. K.M. Arndt, C.M. Kane, Running with RNA polymerase: eukaryotic transcript elongation, Trends Genet. 19 (2003) 543-550.
14. P.J. Costa, K.M. Arndt, Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation, Genetics 156 (2000) 535-547.
15. D.K. Pokholok, N.M. Hannett, R.A. Young, Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo, Mol. Cell 9 (2002) 799-809.
16. J.D. Carpten, C.M. Robbins, A. Villablanca, L. Forsberg, S. Presciuttini, J. Bailey-Wilson, W.F. Simonds, E.M. Gillanders, A.M. Kennedy, J.D. Chen, S.K. Agarwal, R. Sood, M.P. Jones, T.Y. Moses, C. Haven, D. Petillo, P.D. Leotlela, B. Harding, D. Cameron, A.A. Pannett, A. Hoog, H. Heath III, L.A. James-Newton, B. Robinson, R.J. Zarbo, B.M. Cavaco, W. Wassif, N.D. Perrier, I.B. Rosen, U. Kristoffersson, P.D. Turnpenny, L.O. Farnebo, G.M. Besser, C.E. Jackson,H.Morreau, J.M. Trent, R.V. Thakker, S.J.Marx, B.T. Teh, C. Larsson, M.R. Hobbs, HRPT2, encoding parafibromin, is mutated in hyperparathyroidism-jaw tumor syndrome, Nat. Genet. 32 (2002) 676-680.
17. O. Rozenblatt-Rosen, C.M. Hughes, S.J. Nannepaga, K.S. Shanmugam, T.D. Copeland, T. Guszczynski, J.H. Resau, M. Meyerson, The parafibromin tumor suppressor protein is part of a human Paf1 complex, Mol. Cell. Biol. 25 (2005) 612-620.
18. A. Yart, M. Gstaiger, C. Wirbelauer, M. Pecnik, D. Anastasiou, D. Hess, W. Krek, The HRPT2 tumor suppressor gene product parafibromin associates with human PAF1 and RNA polymerase II, Mol. Cell. Biol. 25 (2005) 5052-5060.
19. B. Zhu, S.S. Mandal, A.D. Pham, Y. Zheng, H. Erdjument-Bromage, S.K. Batra, P. Tempst, D. Reinberg, The human PAF complex coordinates transcription with events downstream of RNA synthesis, Genes Dev. 19 (2005) 1668-1673.
20. J. Kim, M. Guermah, R.G. Roeder, The Human Paf1 Complex Acts in Chromatin Transcription Elongation Both Independently and Cooperatively with SII/TFIIS, Cell 140 (2010) 491-503.
21. K. Adelman, W. Wei, M.B. Ardehali, J. Werner, B. Zhu, D. Reinberg, J.T. Lis, Drosophila Paf1 modulates chromatin structure at actively transcribed genes, Mol. Cell. Biol. 26 (2006) 250-260.
22. K. Nordick, M.G. Hoffman, J.L. Betz, J.A. Jaehning, 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 (2008) 1158-1167.
23. L. Ding, M. Paszkowski-Rogacz, A. Nitzsche, M.M. Slabicki, A.K. Heninger, I. de Vries, R. Kittler, M. Junqueira, A. Shevchenko, H. Schulz, N. Hubner, M.X. Doss, A. Sachinidis, J. Hescheler, R. Iacone, K. Anastassiadis, A.F. Stewart, M.T. Pisabarro, A. Caldarelli, I. Poser, M. Theis, F. Buchholz, A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity, Cell Stem Cell 4 (2009) 403-415.
24. O. Rozenblatt-Rosen, T. Nagaike, J.M. Francis, S. Kaneko, K.A. Glatt, C.M. Hughes, T. LaFramboise, J.L. Manley, M. Meyerson, The tumor suppressor Cdc73 functionally associateswith CPSF and CstF 3′mRNA processing factors, Proc. Natl. Acad. Sci. USA 106 (2009) 755-760.
25. Y. Chen, Y. Yamaguchi, Y. Tsugeno, J. Yamamoto, T. Yamada, M. Nakamura, K. Hisatake, H. Handa, DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation, Genes Dev. 23 (2009) 2765-2777.
26. C. Mosimann, G. Hausmann, K. Basler, Parafibromin/Hyrax activates Wnt/Wg target gene transcription by direct association with beta-catenin/Armadillo, Cell 125 (2006) 327-341.
27. C. Mosimann, G. Hausmann, K. Basler, The role of Parafibromin/Hyrax as a nuclear Gli/Ci-interacting protein in Hedgehog target gene control, Mech. Dev. 126 (2009) 394-405.
28. M.Y. Youn, H.S. Yoo, M.J. Kim, S.Y. Hwang, Y.W. Choi, S.V. Desiderio, J.Y. Yoo, hCTR9, a component of PAF1 complex, participates in the transcription of IL-6 responsive genes through regulation of STAT3-DNA interactions, J. Biol. Chem. 282 (2007) 34727-34734.
29. L. Lin, J.H. Zhang, L.M. Panicker, W.F. Simonds, The parafibromin tumor suppressor protein inhibits cell proliferation by repression of the c-myc protooncogene, Proc. Natl. Acad. Sci. USA 105 (2008) 17420-17425.
30. A.D.Mozdy, E.R. Podell, T.R. Cech, Multiple yeast genes, including Paf1 complex genes, affect telomere length via telomerase RNA abundance, Mol. Cell. Biol. 28 (2008) 4152-4161.
31. P.J. Newey, M.R. Bowl, R.V. Thakker, Parafibromin-functional insights, J. Intern. Med. 266 (2009) 84-98.
32. G.E. Woodard, L. Lin, J.H. Zhang, S.K. Agarwal, S.J. Marx, W.F. Simonds, Parafibromin, product of the hyperparathyroidism-jaw tumor syndrome gene HRPT2, regulates cyclin D1/PRAD1 expression, Oncogene 24 (2005) 1272-1276.
33. K. Chaudhary, S. Deb, N. Moniaux, M.P. Ponnusamy, S.K. Batra, Human RNA polymerase II-associated factor complex: dysregulation in cancer, Oncogene 26 (2007) 7499-7507.
34. N. Moniaux, C. Nemos, B.M. Schmied, S.C. Chauhan, S. Deb, K. Morikane, A. Choudhury,M. Vanlith, M. Sutherlin, J.M. Sikela,M.A. Hollingsworth, S.K. Batra, The human homologue of the RNA polymerase II-associated factor 1 (hPaf1), localized on the 19q13 amplicon, is associated with tumorigenesis, Oncogene 25 (2006) 3247-3257.
35. P.Wang,M.R. Bowl, S. Bender, J. Peng, L. Farber, J. Chen, A. Ali, Z. Zhang, A.S. Alberts, R.V. Thakker, A. Shilatifard, B.O. Williams, B.T. Teh, Parafibromin, a component of the human PAF complex, regulates growth factors and is required for embryonic development and survival in adult mice, Mol. Cell. Biol. 28 (2008) 2930-2940.
36. N. Moniaux, C. Nemos, S. Deb, B. Zhu, I. Dornreiter, M.A. Hollingsworth, S.K. Batra, The human RNA polymerase II-associated factor 1 (hPaf1): a new regulator of cell-cycle progression, PloS One 4 (2009) e7077.
37. S. Krishnamurthy, M. Hampsey, Eukaryotic transcription initiation, Curr. Biol. 19 (2009) R153-R156.
38. T.W. Sikorski, S. Buratowski, The basal initiation machinery: beyond the general transcription factors, Curr. Opin. Cell Biol. 21 (2009) 344-351.
39. A. Shilatifard, Transcriptional elongation control by RNA polymerase II: a new frontier, Biochim. Biophys. Acta 1677 (2004) 79-86.
40. N. Proudfoot, New perspectives on connecting messenger RNA 3′ end formation to transcription, Curr. Opin. Cell. Biol. 16 (2004) 272-278.
41. E. Rosonina, S. Kaneko, J.L. Manley, Terminating the transcript: breaking up is hard to do, Genes Dev. 20 (2006) 1050-1056.
42. P. Richard, J.L. Manley, Transcription termination by nuclear RNA polymerases, Genes Dev. 23 (2009) 1247-1269.
43. H.P. Phatnani, A.L. Greenleaf, Phosphorylation and functions of the RNA polymerase II CTD, Genes Dev. 20 (2006) 2922-2936.
44. Y. Hirose, Y. Ohkuma, Phosphorylation of the C-terminal domain of RNA polymerase II plays central roles in the integrated events of eucaryotic gene expression, J. Biochem. 141 (2007) 601-608.
45. S. Buratowski, Progression through the RNA polymerase II CTD cycle, Mol. Cell 36 (2009) 541-546.
46. M.S. Akhtar, M. Heidemann, J.R. Tietjen, D.W. Zhang, R.D. Chapman, D. Eick, A.Z. Ansari, TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II, Mol. Cell 34 (2009) 387-393.
47. E.I. Kanin, R.T. Kipp, C. Kung, M. Slattery, A. Viale, S. Hahn, K.M. Shokat, A.Z. Ansari, Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis, Proc. Natl. Acad. Sci. USA 104 (2007) 5812-5817.
48. S.W. Hong, S.M. Hong, J.W. Yoo, Y.C. Lee, S. Kim, J.T. Lis, D.K. Lee, Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome, Proc. Natl. Acad. Sci. USA 106 (2009) 14276-14280.
49. A. Wood, A. Shilatifard, Bur1/Bur2 and the Ctk complex in yeast: the split personality of mammalian P-TEFb, Cell Cycle (2006) 1066-1068.
50. H. Qiu, C.Hu, A.G.Hinnebusch, Phosphorylation of the Pol II CTDby KIN28 enhances BUR1/BUR2 recruitment and Ser2 CTD phosphorylation near promoters, Mol. Cell 33 (2009) 752-762.
51. S.H. Ahn, M.C. Keogh, S. Buratowski, Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II, EMBO J. 28 (2009) 205-212.
52. C.L. Mueller, S.E. Porter, M.G. Hoffman, J.A. Jaehning, The Paf1 complex has functions independent of actively transcribing RNA polymerase II, Mol. Cell 14 (2004) 447-456.
53. M. Kim, S.H. Ahn, N.J. Krogan, J.F. Greenblatt, S. Buratowski, Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes, EMBO J. 23 (2004) 354-364.
54. C.D. Kaplan, M.J. Holland, F. Winston, Interaction between transcription elongation factors and mRNA 3′-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus, J. Biol. Chem. 280 (2005) 913-922.
55. H. Qiu, C. Hu, C.M. Wong, A.G. Hinnebusch, The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II, Mol. Cell. Biol. 26 (2006) 3135-3148.
56. J.M. O'Sullivan, S.M. Tan-Wong, A. Morillon, B. Lee, J. Coles, J. Mellor, N.J. Proudfoot, Gene loops juxtapose promoters and terminators in yeast, Nat. Genet. 36 (2004) 1014-1018.
57. A. Ansari, M. Hampsey, A role for the CPF 3′-end processing machinery in RNAP II-dependent gene looping, Genes Dev. 19 (2005) 2969-2978.
58. B.N. Singh, M. Hampsey, A transcription-independent role for TFIIB in gene looping, Mol. Cell. Biol. 27 (2007) 806-816.
59. J.P. Laine, B.N. Singh, S. Krishnamurthy, M. Hampsey, A physiological role for gene loops in yeast, Genes Dev. 23 (2009) 2604-2609.
60. S.M. Tan-Wong, H.D.Wijayatilake, N.J. Proudfoot, Gene loops function to maintain transcriptionalmemory through interaction with the nuclear pore complex, Genes Dev. 23 (2009) 2610-2624.
61. M. Gerber, A. Shilatifard, Transcriptional elongation by RNA polymerase II and histone methylation, J. Biol. Chem. 278 (2003) 26303-26306.
62. S.M. Fuchs, R.N. Laribee, B.D. Strahl, Protein modifications in transcription elongation, Biochim. Biophys. Acta 1789 (2009) 26-36.
63. Y. Liu, L.Warfield, C. Zhang, J. Luo, J. Allen,W.H. Lang, J. Ranish, K.M. Shokat, S.Hahn, Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex, Mol. Cell. Biol. 29 (2009) 4852-4863.
64. J.C. Jones, H.P. Phatnani, T.A. Haystead, J.A. MacDonald, S.M. Alam, A.L. Greenleaf, C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats, J. Biol. Chem. 279 (2004) 24957-24964.
65. H.P. Phatnani, J.C. Jones, A.L. Greenleaf, Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome, Biochemistry 43 (2004) 15702-15719.
66. S.H. Ahn, M. Kim, S. Buratowski, Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end-processing, Mol. Cell 13 (2004) 67-76.
67. R.N. Laribee, N.J. Krogan, T. Xiao, Y. Shibata, T.R. Hughes, J.F. Greenblatt, B.D. Strahl, BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex, Curr. Biol. 15 (2005) 1487-1493.
68. Y. Chu, R. Simic, M.H. Warner, K.M. Arndt, G. Prelich, Regulation of histone modification and cryptic transcription by the Bur1 and Paf1 complexes, EMBO J. 26 (2007) 4646-4656.
69. K. Zhou, W.H. Kuo, J. Fillingham, J.F. Greenblatt, Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5, Proc. Natl. Acad. Sci. USA 106 (2009) 6956-6961.
70. R. Pavri, B. Zhu, G. Li, P. Trojer, S. Mandal, A. Shilatifard, D. Reinberg, Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II, Cell 125 (2006) 703-717.
71. K.W. Mulder, A.B. Brenkman, A. Inagaki, N.J. van den Broek, H.T. Timmers, Regulation of histone H3K4 tri-methylation and PAF complex recruitment by the Ccr4-Not complex, Nucleic Acids Res. 35 (2007) 2428-2439.
72. B. Li, M. Carey, J.L. Workman, The role of chromatin during transcription, Cell 128 (2007) 707-719.
73. A. Shilatifard, Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation, Curr. Opin. Cell Biol. 20 (2008) 341-348.
74. Z. Wang, D.E. Schones, K. Zhao, Characterization of human epigenomes, Curr. Opin. Genet. Dev. 19 (2009) 127-134.
75. T. Kim, S. Buratowski, Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5′ transcribed regions, Cell 137 (2009) 259-272.
76. N.J. Krogan, J. Dover, A. Wood, J. Schneider, J. Heidt, M.A. Boateng, K. Dean, O.W. Ryan, A. Golshani, M. Johnston, J.F. Greenblatt, A. Shilatifard, The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation, Mol. Cell 11 (2003) 721-729.
77. H.H. Ng, F. Robert, R.A. Young, K. Struhl, Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity, Mol. Cell 11 (2003) 709-719.
78. A. Wood, J. Schneider, J. Dover, M. Johnston, A. Shilatifard, The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p, J. Biol. Chem. 278 (2003) 34739-34742.
79. T. Xiao, C.F. Kao, N.J. Krogan, Z.W. Sun, J.F. Greenblatt, M.A. Osley, B.D. Strahl, Histone H2B ubiquitylation is associated with elongating RNA polymerase II, Mol. Cell. Biol. 25 (2005) 637-651.
80. B. Zhu, Y. Zheng, A.D. Pham, S.S. Mandal, H. Erdjument-Bromage, P. Tempst, D. Reinberg, Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation, Mol. Cell 20 (2005) 601-611.
81. J. Kim, M. Guermah, R.K. McGinty, J.S. Lee, Z. Tang, T.A. Milne, A. Shilatifard, T.W. Muir, R.G. Roeder, RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells, Cell 137 (2009) 459-471.
82. T. Xiao, H. Hall, K.O. Kizer, Y. Shibata, M.C. Hall, C.H. Borchers, B.D. Strahl, Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast, Genes Dev. 17 (2003) 654-663.
83. N.J. Krogan,M. Kim, A. Tong, A. Golshani, G. Cagney, V. Canadien, D.P. Richards, B.K. Beattie, A.Emili, C. Boone, A. Shilatifard, S. Buratowski, J. Greenblatt, Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II, Mol. Cell. Biol. 23 (2003) 4207-4218.
84. K.O. Kizer, H.P. Phatnani, Y. Shibata, H. Hall, A.L. Greenleaf, B.D. Strahl, A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation, Mol. Cell. Biol. 25 (2005) 3305-3316.
85. H.H. Ng, S. Dole, K. Struhl, The Rtf1 component of the Paf1 transcriptional elongation complex is required for ubiquitination of histone H2B, J. Biol. Chem. 278 (2003) 33625-33628.
86. M.H. Warner, K.L. Roinick, K.M. Arndt, Rtf1 is a multifunctional component of the Paf1 complex that regulates gene expression by directing cotranscriptional histone modification, Mol. Cell. Biol. 27 (2007) 6103-6115.
87. K. Tenney, M. Gerber, A. Ilvarsonn, J. Schneider, M. Gause, D. Dorsett, J.C. Eissenberg, A. Shilatifard, Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling, Proc. Natl. Acad. Sci. USA 103 (2006) 11970-11974.
88. S. Oh, H. Zhang, P. Ludwig, S. van Nocker, A mechanism related to the yeast transcriptional regulator Paf1c is required for expression of the Arabidopsis FLC/ MAF MADS box gene family, Plant Cell 16 (2004) 2940-2953.
89. Y. He, M.R. Doyle, R.M. Amasino, PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis, Genes Dev. 18 (2004) 2774-2784.
90. L. Xu, Z. Zhao, A. Dong, L. Soubigou-Taconnat, J.P. Renou, A. Steinmetz, W.H. Shen, Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana, Mol. Cell. Biol. 28 (2008) 1348-1360.
91. A. Wyce, T. Xiao, K.A. Whelan, C. Kosman, W. Walter, D. Eick, T.R. Hughes, N.J. Krogan, B.D. Strahl, S.L. Berger, H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal byUbp8within a SAGA-related complex, Mol. Cell 27 (2007) 275-288.
92. J.L. Betz, M. Chang, T.M. Washburn, S.E. Porter, C.L. Mueller, J.A. Jaehning, 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 (2002) 272-285.
93. M.B. Ardehali, J. Yao, K. Adelman, N.J. Fuda, S.J. Petesch, W.W. Webb, J.T. Lis, Spt6 enhances the elongation rate of RNA polymerase II in vivo, EMBO J. 28 (2009) 1067-1077.
94. A.G. Rondon, M. Gallardo, M. Garcia-Rubio, A. Aguilera, Molecular evidence indicating that the yeast PAF complex is required for transcription elongation, EMBO Rep. 5 (2004) 47-53.
95. R.W.J.West, B. Kruger, S. Thomas, J. Ma, E. Milgrom, RLR1 (THO2), required for expressing lacZ fusions in yeast, is conserved from yeast to humans and is a suppressor of SIN4, Gene 243 (Feb 8 2000) 195-205.
96. R.W. West, E. Milgrom, DEAD-box RNA helicase Sub2 is required for expression of lacZ fusions in Saccharomyces cerevisiae and is a dosage-dependent suppressor of RLR1 (THO2), Gene 288 (2002) 19-27.
97. R. Russnak, K.W. Nehrke, T. Platt, REF2 encodes an RNA-binding protein directly involved in yeast mRNA 3′-end formation, Mol. Cell. Biol. 15 (1995) 1689-1697.
98. K.L. Penheiter, T.M. Washburn, S.E. Porter, M.G. Hoffman, J.A. Jaehning, A posttranscriptional role for the yeast Paf1-RNA polymerase II complex is revealed by identification of primary targets, Mol. Cell 20 (2005) 213-223.
99. L.A. Strawn, C.A. Lin, E.M. Tank, M.M. Osman, S.A. Simpson, H.L. True, Mutants of the Paf1 complex alter phenotypic expression of the yeast prion [PSI+], Mol. Biol. Cell 20 (2009) 2229-2241.
100. Y. Zhang, M.L. Sikes, A.L. Beyer, D.A. Schneider, The Paf1 complex is required for efficient transcription elongation by RNA polymerase I, Proc. Natl. Acad. Sci. USA 106 (2009) 2153-2158.
101. H. Cheng, X. He, C.Moore, The essentialWD repeat protein Swd2 has dual functions in RNA polymerase II transcription termination and lysine 4methylation of histone H3, Mol. Cell. Biol. 24 (2004) 2932-2943.
102. A. Meinhart, P. Cramer, Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors, Nature 430 (2004) 223-226.
103. K.E. Sheldon, D.M. Mauger, K.M. Arndt, A requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3′ end formation, Mol. Cell 20 (2005) 225-236.
104. E.J. Steinmetz, N.K. Conrad, D.A. Brow, J.L. Corden, RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts, Nature 413 (2001) 327-331.
105. S.E. Porter, K.L. Penheiter, J.A. Jaehning, Separation of the Saccharomyces cerevisiae Paf1 complex from RNA polymerase II results in changes in its subnuclear localization, Eukaryot. Cell 4 (2005) 209-220.
106. J. Kim, R.G. Roeder, Direct Bre1-Paf1 complex interactions and RING fingerindependent Bre1-Rad6 interactions mediate H2B ubiquitylation in yeast, J. Biol. Chem. 284 (2009) 20582-20592.
107. R. Simic, D.L. Lindstrom, H.G. Tran, K.L. Roinick, P.J. Costa, A.D. Johnson, G.A. Hartzog, K.M. Arndt, Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes, EMBO J. 22 (2003) 1846-1856.
108. C. Alen, N.A. Kent, H.S. Jones, J. O'Sullivan, A. Aranda, N.J. Proudfoot, A role for chromatin remodeling in transcriptional termination by RNA polymerase II, Mol. Cell 10 (2002) 1441-1452.
109. H. Yu, P. Braun, M.A. Yildirim, I. Lemmens, K. Venkatesan, J. Sahalie, T. Hirozane-Kishikawa, F. Gebreab, N. Li, N. Simonis, T. Hao, J.F. Rual, A. Dricot, A. Vazquez, R.R. Murray, C. Simon, L. Tardivo, S. Tam,N. Svrzikapa, C. Fan,A.S. de Smet, A.Motyl,M.E. Hudson, J. Park, X. Xin, M.E. Cusick, T. Moore, C. Boone, M. Snyder, F.P. Roth, A.L. Barabasi, J. Tavernier, D.E. Hill, M. Vidal, High-quality binary protein interaction map of the yeast interactome network, Science 322 (2008) 104-110.
110. Y. Shi, D.C. Di Giammartino, D. Taylor, A. Sarkeshik, W.J. Rice, J.R. Yates III, J. Frank, J.L. Manley, Molecular architecture of the human pre-mRNA 3′ processing complex, Mol. Cell 33 (2009) 365-376.
111. M.C. Keogh, V. Podolny, S. Buratowski, Bur1 kinase is required for efficient transcription elongation by RNA polymerase II, Mol. Cell. Biol. 23 (2003) 7005-7018.
112. S. Rother, K. Strasser, The RNA polymerase II CTD kinase Ctk1 functions in translation elongation, Genes Dev. 21 (2007) 1409-1421.
113. G.M. Wilmes, M. Bergkessel, S. Bandyopadhyay, M. Shales, H. Braberg, G. Cagney, S.R. Collins, G.B. Whitworth, T.L. Kress, J.S. Weissman, T. Ideker, C. Guthrie, N.J. Krogan, A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing, Mol. Cell 32 (2008) 735-746.
114. K. Tarassov, V. Messier, C.R. Landry, S. Radinovic, M.M. Serna Molina, I. Shames, Y. Malitskaya, J. Vogel, H. Bussey, S.W. Michnick, An in vivo map of the yeast protein interactome, Science 320 (2008) 1465-1470.