PAF1/YBR279W Summary Help

Standard Name PAF1 1
Systematic Name YBR279W
Feature Type ORF, Verified
Description Component of the Paf1p complex involved in transcription elongation; binds to and modulates the activity of RNA polymerases I and II; required for expression of a subset of genes, including cell cycle-regulated genes; involved in SER3 repression by helping to maintain SRG1 transcription-dependent nucleosome occupancy; homolog of human PD2/hPAF1 (2, 3, 4, 5, 6, 7 and see Summary Paragraph)
Name Description RNA Polymerase II Associated Factor 1
Chromosomal Location
ChrII:761257 to 762594 | ORF Map | GBrowse
Gene Ontology Annotations All PAF1 GO evidence and references
  View Computational GO annotations for PAF1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Targets 53 genes
Regulators 1 genes
Classical genetics
Large-scale survey
264 total interaction(s) for 144 unique genes/features.
Physical Interactions
  • Affinity Capture-Luminescence: 2
  • Affinity Capture-MS: 73
  • Affinity Capture-RNA: 4
  • Affinity Capture-Western: 38
  • Co-fractionation: 2
  • Co-localization: 1
  • Co-purification: 1
  • PCA: 1
  • Protein-RNA: 4
  • Reconstituted Complex: 1
  • Two-hybrid: 3

Genetic Interactions
  • Dosage Rescue: 4
  • Negative Genetic: 46
  • Phenotypic Enhancement: 5
  • Phenotypic Suppression: 5
  • Positive Genetic: 5
  • Synthetic Growth Defect: 17
  • Synthetic Haploinsufficiency: 1
  • Synthetic Lethality: 36
  • Synthetic Rescue: 15

Expression Summary
Length (a.a.) 445
Molecular Weight (Da) 51,800
Isoelectric Point (pI) 4.63
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrII:761257 to 762594 | ORF Map | GBrowse
Last Update Coordinates: 2011-02-03 | Sequence: 1997-01-28
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1338 761257..762594 2011-02-03 1997-01-28
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000483

Paf1p is a nuclear RNA polymerase II-associated factor important for cell growth and required for full expression of a subset of cell cycle-regulated genes (8, 9, 10, 2). Yeast contains at least two complex forms of RNA polymerase II (Pol II), one including the SRBps (Srb2p, Srb4p, Srb5p, Srb6p, Srb7p, Srb8p) and a second biochemically distinct form defined by the presence of Paf1p and Cdc73p (10). The Cdc73p-Paf1p-Pol II-containing complex (Paf1p complex) also includes Ctr9p, Rtf1p, Leo1p, Gal11p, Ccr4p, Hpr1p, and the general initiation factors TFIIB and TFIIF, but lacks Tbp1p, TFIIH, and transcription elongation factor TFIIS, as well as the SRBps (3). It appears to function during elongation in conjunction with Spt4p-Spt5p and Spt16p-Pob3p (11). The human homolog of yeast Paf1p is hPaf1, a pancreatic differentiation 2 (PD2) gene that has been shown to be associated with tumorigenesis (4).

The Paf1p complex acts in the same pathway as the Pkc1p-Slt2p MAP kinase cascade and is required for full expression of many cell wall biosynthetic genes (10, 12). The complex is also required for the interaction of Rad6p and COMPASS with RNA polymerase II and for monoubiquitination of histone H2B at promoters (13). Further, the Paf1p complex is required for histone H3 methylation at lysines 4 and 79, thereby linking transcriptional elongation to chromatin methylation (14).

Disruption of PAF1 leads to pleiotropic phenotypic traits, including slow growth, temperature sensitivity, and abnormal cell morphology, as well as decreased induction of the galactose-regulated genes, and greatly increased induction of MAK16 (8). Deletion leads to elevated recombination between direct repeats (10), a defective Paf1p complex, and a block in transcription, which is relieved by removal of Leo1p or Rtf1p (2). Loss of Paf1p is lethal in combination with loss of Swi4p or Swi6p, and overexpression of either Swi4p or Mbp1p suppresses some paf1 phenotypes (12).

Last updated: 2007-03-21 Contact SGD

References cited on this page View Complete Literature Guide for PAF1
1) Wade PA, et al.  (1996) A novel collection of accessory factors associated with yeast RNA polymerase II. Protein Expr Purif 8(1):85-90
2) Mueller CL and Jaehning JA  (2002) Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol Cell Biol 22(7):1971-80
3) Betz JL, 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(2):272-85
4) Moniaux N, et al.  (2006) The human homologue of the RNA polymerase II-associated factor 1 (hPaf1), localized on the 19q13 amplicon, is associated with tumorigenesis. Oncogene 25(23):3247-57
5) Zhang Y, et al.  (2009) The Paf1 complex is required for efficient transcription elongation by RNA polymerase I. Proc Natl Acad Sci U S A 106(7):2153-8
6) Tous C, et al.  (2011) A novel assay identifies transcript elongation roles for the Nup84 complex and RNA processing factors. EMBO J 30(10):1953-64
7) Pruneski JA, et al.  (2011) The Paf1 complex represses SER3 transcription in Saccharomyces cerevisiae by facilitating intergenic transcription-dependent nucleosome occupancy of the SER3 promoter. Eukaryot Cell 10(10):1283-94
8) Shi X, et al.  (1996) Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription. Mol Cell Biol 16(2):669-76
9) Shi X, et al.  (1997) Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Mol Cell Biol 17(3):1160-9
10) 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(2):1056-67
11) Squazzo SL, et al.  (2002) The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J 21(7):1764-74
12) Porter SE, et al.  (2002) The yeast pafl-rNA polymerase II complex is required for full expression of a subset of cell cycle-regulated genes. Eukaryot Cell 1(5):830-42
13) 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(37):34739-42
14) 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(3):721-9