The Paf1 complex is required for efficient transcription elongation by RNA polymerase I

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 7, 2009, Pages 2153-2158

  Zhang, Yinfeng ^a   Sikes, Martha L ^b   Beyer, Ann L ^b   Schneider, David A ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b UNIVERSITY OF VIRGINIA HEALTH SYSTEM   (United States)

Author keywords

Gene expression; Ribosome

Indexed keywords

DNA DIRECTED RNA POLYMERASE; PAF1 ENZYME; RNA POLYMERASE II; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; DNA TRANSCRIPTION; ENZYME SUBUNIT; GENE DELETION; NONHUMAN; PRIORITY JOURNAL; RNA SYNTHESIS; WILD TYPE;

BIOCHEMICAL PROCESSES; DNA POLYMERASE I; DNA PRIMERS; DNA, RIBOSOMAL; GENE DELETION; GENE EXPRESSION REGULATION, FUNGAL; MODELS, BIOLOGICAL; NUCLEAR PROTEINS; PLASMIDS; RNA POLYMERASE I; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

EID: 60549089376     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0812939106     Document Type: Article

References (43)

1. Wade CH, Umbarger MA, McAlear MA (2006) The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes. Yeast 23:293-306.
2. Venema J, Tollervey D (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311.
3. Warner JR (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24:437-440.
4. Claypool JA, et al. (2004) Tor pathway regulates Rrn3p-dependent recruitment of yeast RNA polymerase I to the promoter but does not participate in alteration of the number of active genes. Mol Biol Cell 15:946-956.
5. Mayer C, Zhao J, Yuan X, Grummt I (2004) mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes Dev 18:423-434.
6. Stefanovsky V, et al. (2006) Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF phosphorylation and r-chromatin remodeling. Mol Cell 21:629-639.
7. Schneider DA, et al. (2007) Transcription elongation by RNA polymerase I is linked to efficient rRNA processing and ribosome assembly. Mol Cell 26:217-229.
8. Schnapp G, Graveley BR, Grummt I (1996) TFIIS binds to mouse RNA polymerase I and stimulates transcript elongation and hydrolytic cleavage of nascent rRNA. Mol Gen Genet 252:412-419.
9. Fath S, et al. (2004) Dephosphorylation of RNA polymerase I by Fcp1p is required for efficient rRNA synthesis. J Biol Chem 279:25251-25259.
10. Bouchoux C, et al. (2004) CTD kinase I is involved in RNA polymerase I transcription. Nucleic Acids Res 32:5851-5860.
11. Schneider DA, et al. (2006) RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci USA 103:12707-12712.
12. Sims RJ, III, Belotserkovskaya R, Reinberg D (2004) Elongation by RNA polymerase II: The short and long of it. Genes Dev 18:2437-2468.
13. Krogan NJ, et al. (2002) RNA polymerase II elongation factors of Saccharomyces cerevisiae: A targeted proteomics approach. Mol Cell Biol 22:6979-6992.
14. Mueller CL, Jaehning JA (2002) Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol Cell Biol 22:1971-1980.
15. Mueller CL, Porter SE, Hoffman MG, Jaehning JA (2004) The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol Cell 14:447-456.
16. Squazzo SL, et al. (2002) The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J 21:1764-1774.
17. Qiu H, Hu C, Wong CM, Hinnebusch AG (2006) The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Mol Cell Biol 26:3135-3148.
18. Rondón AG, Gallardo M, García-Rubio M, Aguilera A (2004) Molecular evidence indicating that the yeast PAF complex is required for transcription elongation. EMBO Rep 5:47-53.
19. Wood A, et al. (2003) 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 278:34739-34742.
20. Krogan NJ, 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.
21. Adelman K, et al. (2006) Drosophila Paf1 modulates chromatin structure at actively transcribed genes. Mol Cell Biol 26:250-260.
22. Stolinski LA, Eisenmann DM, Arndt KM (1997) Identification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae. Mol Cell Biol 17:4490-4500.
23. Nordick KM, Hoffman MG, Betz JL, Jaehning JA (2008) Direct interactions between the Paf1 complex and a cleavage and polyadenylation factor are revealed by dissociation of Paf1 from RNA polymerase II. Eukaryotic Cell 7:1158-1167.
24. Sheldon KE, Mauger DM, Arndt KM (2005) A requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3′ end formation. Mol Cell 20:225-236.
25. Porter SE, Penheiter KL, Jaehning JA (2005) Separation of the Saccharomyces cerevisiae Paf1 complex from RNA polymerase II results in changes in its subnuclear localization. Eukaryotic Cell 4:209-220.
26. Jones HS, et al. (2007) RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. Nat Struct Mol Biol 14:123-130.
27. French SL, et al. (2008) Visual analysis of the yeast 5S rRNA gene transcriptome: Regulation and role of La protein. Mol Cell Biol 28:4576-4587.
28. Kobayashi T, Ganley AR (2005) Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science 309:1581-1584.
29. Warner JR (1991) Labeling of RNA and phosphoproteins in Saccharomyces cerevisiae. Methods Enzymol 194:423-428.
30. Mason PB, Struhl K (2005) Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell 17:831-840.
31. Oakes M, et al. (1999) Transcription factor UAF, expansion, and contraction of ribosomal DNA (rDNA) repeats, and RNA polymerase switch in transcription of yeast rDNA. Mol Cell Biol 19:8559-8569.
32. Kim, Y.-H., et al. (2006) Chromosome XII context is important for rDNA function in yeast. Nucleic Acids Res 34:2914-2924.
33. Kobayashi T, Heck DJ, Nomura M, Horiuchi T (1998) Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: Requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev 12:3821-3830.
34. French SL, et al. (2003) In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol Cell Biol 23:1558-1568.
35. Osheim YN, et al. (2004) Pre-18S ribosomal RNA is structurally compacted into the SSU processome prior to being cleaved from nascent transcripts in Saccharomyces cerevisiae. Mol Cell 16:943-954.
36. Powell W, Reines D (1996) Mutations in the second largest subunit of RNA polymerase II cause 6-azauracil sensitivity in yeast and increased transcriptional arrest in vitro. J Biol Chem 271:6866-6873.
37. Chang M, et al. (1999) A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol Cell Biol 19:1056-1067.
38. Mueller JE, Canze M, Bryk M (2006) The requirements for COMPASS and Paf1 in transcriptional silencing and methylation of histone H3 in Saccharomyces cerevisiae. Genetics 173:557-567.
39. Zhu B, et al. (2005) The human PAF complex coordinates transcription with events downstream of RNA synthesis. Genes Dev 19:1668-1673.
40. Woodard GE, et al. (2004) Parafibromin, product of the hyperparathyroidism-jaw tumor syndrome gene HRPT2, regulates cyclin D1/PRAD1 expression. Oncogene 24:1272-1276.
41. Rozenblatt-Rosen O, et al. (2005) The parafibromin tumor suppressor protein is part of a human Paf1 complex. Mol Cell Biol 25:612-620.
42. Cioci F, et al. (2003) Silencing in yeast rDNA chromatin: Reciprocal relationship in gene expression between RNA polymerase I and II. Mol Cell 12:135-145.
43. Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.