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Gene Review

PAF1  -  Paf1p

Saccharomyces cerevisiae S288c

Synonyms: Protein PAF1, RNA polymerase II-associated protein 1, YBR2016, YBR279W
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High impact information on PAF1

  • Instead, Paf1 loss altered poly(A) site utilization of primary target genes SDA1 and MAK21, resulting in increased abundance of 3'-extended mRNAs [1].
  • The Paf1 complex associates with and facilitates Nrd1 recruitment to the SNR47 gene, suggesting a direct involvement in 3' end formation [2].
  • Our results reveal a posttranscriptional function for the Paf1 complex, which appears unrelated to its role in histone methylation [2].
  • Loss of Paf1 factors causes a reduction of Pol II Ser2 phosphorylation and shortened poly(A) tails, suggesting that the complex facilitates linkage of transcriptional and posttranscriptional events [3].
  • The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation [4].

Biological context of PAF1

  • Deletion of either PAF1 or CTR9 leads to similar severe pleiotropic phenotypes, which are unaltered when the two mutations are combined [5].
  • Mutations in CDC73 and PAF1 affect cell growth and the abundance of transcripts from a subset of yeast genes (X. Shi et al., Mol. Cell. Biol., 1996 16, 669-676) [6].
  • Additionally, as previously observed for hpr1Delta, deleting PAF1 or CDC73 leads to elevated recombination between direct repeats [7].
  • In contrast, the transcript level of MAK16, an essential gene involved in cell cycle regulation, is greatly increased in the paf1 mutant strain [8].
  • Also isolated as RAPs are two proteins (Cdc73p and Paf1p) with interesting connections to gene expression [6].

Anatomical context of PAF1

  • In contrast, the resistance of paf1 Delta cells to the transcription elongation inhibitors 6-azauracil and mycophenolic acid correlates with its ability to derepress the IMD2 transcript [9].
  • The Pafl-RNA polymerase II complex (Paf1 complex) acts in the same pathway as the Pkc1-mitogen-activated protein kinase cascade and is required for full expression of many cell wall biosynthetic genes [10].
  • The peroxisomal integral membrane protein Pay5p is a homologue of mammalian PAF-1 proteins, which are essential for peroxisome assembly and whose mutation in humans results in peroxisome biogenesis disorders [11].

Associations of PAF1 with chemical compounds

  • In particular, disruption of PAF1 decreases the induction of the galactose-regulated genes three- to fivefold [8].
  • Finally, we found that defects in the Paf1 complex cause sensitivity to 6-azauracil and diminished PUR5 induction, properties frequently associated with impaired transcription elongation [12].
  • Paf1 is an RNA polymerase II-associated protein in yeast, which defines a complex that is distinct from the Srb/Mediator holoenzyme [9].
  • For example, paf1 Delta causes sensitivity to hydroxyurea; this phenotype correlates with a reduction in RNR1 transcript abundance and is suppressed by over-expression of RNR1 [9].

Physical interactions of PAF1

  • The phenotypes of mutations in Paf1 complex components are exacerbated in the swi4 Delta background, suggesting that the complex acts in a pathway parallel to that controlled by Swi4 [9].
  • The presence of the Paf1/Cdc73 complex on ORFs in vivo suggests a novel function for this complex in elongation [13].
  • We also show that Paf1 complex is required for the interaction of Rad6 and COMPASS with RNA polymerase II [14].

Regulatory relationships of PAF1

  • The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II [15].
  • Thus, in addition to its role during the elongation phase of transcription, the Paf1 complex appears to activate the function but not the placement of the Rad6-Bre1 ubiquitin-protein ligase at the promoters of active genes [14].

Other interactions of PAF1

  • The Srbps and Cdc73p-Paf1p therefore appear to define two complexes with partially redundant, essential functions in the yeast cell [16].
  • In contrast, in both paf1 and rtf1 strains, the remaining factors are found in the nucleolus as well as the nucleoplasm [17].
  • Like Paf1p, the GAL11 gene product is found associated with RNA polymerase II and is required for regulated expression of many yeast genes including those controlled by galactose [8].
  • RNA polymerase II, TFIIS, Spt5, and, unexpectedly, the Paf1/Cdc73 complex, were found associated with open reading frames [13].
  • Trimethylation requires histone H2B ubiquitylation and the PAF1 complex, which are linked to transcription elongation, but how they activate Set1 is not known [18].


  1. A posttranscriptional role for the yeast Paf1-RNA polymerase II complex is revealed by identification of primary targets. Penheiter, K.L., Washburn, T.M., Porter, S.E., Hoffman, M.G., Jaehning, J.A. Mol. Cell (2005) [Pubmed]
  2. A Requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' end formation. Sheldon, K.E., Mauger, D.M., Arndt, K.M. Mol. Cell (2005) [Pubmed]
  3. The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mueller, C.L., Porter, S.E., Hoffman, M.G., Jaehning, J.A. Mol. Cell (2004) [Pubmed]
  4. The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Krogan, N.J., Dover, J., Wood, A., Schneider, J., Heidt, J., Boateng, M.A., Dean, K., Ryan, O.W., Golshani, A., Johnston, M., Greenblatt, J.F., Shilatifard, A. Mol. Cell (2003) [Pubmed]
  5. Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mueller, C.L., Jaehning, J.A. Mol. Cell. Biol. (2002) [Pubmed]
  6. A novel collection of accessory factors associated with yeast RNA polymerase II. Wade, P.A., Werel, W., Fentzke, R.C., Thompson, N.E., Leykam, J.F., Burgess, R.R., Jaehning, J.A., Burton, Z.F. Protein Expr. Purif. (1996) [Pubmed]
  7. A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Chang, M., French-Cornay, D., Fan, H.Y., Klein, H., Denis, C.L., Jaehning, J.A. Mol. Cell. Biol. (1999) [Pubmed]
  8. Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription. Shi, X., Finkelstein, A., Wolf, A.J., Wade, P.A., Burton, Z.F., Jaehning, J.A. Mol. Cell. Biol. (1996) [Pubmed]
  9. Phenotypic analysis of Paf1/RNA polymerase II complex mutations reveals connections to cell cycle regulation, protein synthesis, and lipid and nucleic acid metabolism. Betz, J.L., Chang, M., Washburn, T.M., Porter, S.E., Mueller, C.L., Jaehning, J.A. Mol. Genet. Genomics (2002) [Pubmed]
  10. The yeast pafl-rNA polymerase II complex is required for full expression of a subset of cell cycle-regulated genes. Porter, S.E., Washburn, T.M., Chang, M., Jaehning, J.A. Eukaryotic Cell (2002) [Pubmed]
  11. Mutations in the PAY5 gene of the yeast Yarrowia lipolytica cause the accumulation of multiple subpopulations of peroxisomes. Titorenko, V.I., Eitzen, G.A., Rachubinski, R.A. J. Biol. Chem. (1996) [Pubmed]
  12. The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. Squazzo, S.L., Costa, P.J., Lindstrom, D.L., Kumer, K.E., Simic, R., Jennings, J.L., Link, A.J., Arndt, K.M., Hartzog, G.A. EMBO J. (2002) [Pubmed]
  13. Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Pokholok, D.K., Hannett, N.M., Young, R.A. Mol. Cell (2002) [Pubmed]
  14. The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. Wood, A., Schneider, J., Dover, J., Johnston, M., Shilatifard, A. J. Biol. Chem. (2003) [Pubmed]
  15. The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Qiu, H., Hu, C., Wong, C.M., Hinnebusch, A.G. Mol. Cell. Biol. (2006) [Pubmed]
  16. Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Shi, X., Chang, M., Wolf, A.J., Chang, C.H., Frazer-Abel, A.A., Wade, P.A., Burton, Z.F., Jaehning, J.A. Mol. Cell. Biol. (1997) [Pubmed]
  17. Separation of the Saccharomyces cerevisiae Paf1 complex from RNA polymerase II results in changes in its subnuclear localization. Porter, S.E., Penheiter, K.L., Jaehning, J.A. Eukaryotic Cell (2005) [Pubmed]
  18. Histone trimethylation by Set1 is coordinated by the RRM, autoinhibitory, and catalytic domains. Schlichter, A., Cairns, B.R. EMBO J. (2005) [Pubmed]
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