PAF1 / YBR279W Overview

Standard Name
PAF1 1
Systematic Name
Feature Type
ORF , Verified
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
Name Description
RNA Polymerase II Associated Factor 1
Comparative Info
Sequence Details


The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.

Protein Details


Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.

Length (a.a.)
Mol. Weight (Da)
Isoelectric Point
Median Abundance (molecules/cell)
5232 +/- 1675
Half-life (hr)


Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.

View all PAF1 alleles in SGD search

Gene Ontology Details

Gene Ontology

GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.

Non-DNA binding transcription factor; subunit of the Cdc73/Paf1 transcription elongation complex; regulates transcription from Pol I and II promoters; also involved in snoRNA 3'-end processing

View computational annotations

Cellular Component

Manually Curated


Macromolecular complex annotations are imported from the Complex Portal. These annotations have been derived from physical molecular interaction evidence extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background.

Phenotype Details


Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.

Disease Details


Disease Annotations consist of three mandatory components: a gene product, a term from the Disease Ontology (DO) controlled vocabulary and an evidence code. SGD provides manually curated DO Annotations derived from the literature. Click "Disease Details" to view all Disease information and evidence for this locus as well as diseases it shares with other genes.

Yeast PAF1 is homologous to human PAF1, and has been used to study pancreatic oncogenesis

Manually Curated

Interaction Details


Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.

372 total interactions for 200 unique genes

Physical Interactions

  • Affinity Capture-Luminescence: 2
  • Affinity Capture-MS: 109
  • Affinity Capture-RNA: 9
  • Affinity Capture-Western: 58
  • Biochemical Activity: 2
  • Co-crystal Structure: 2
  • Co-fractionation: 2
  • Co-localization: 2
  • Co-purification: 2
  • PCA: 1
  • Protein-RNA: 4
  • Reconstituted Complex: 14
  • Two-hybrid: 3

Genetic Interactions

  • Dosage Rescue: 4
  • Negative Genetic: 47
  • Phenotypic Enhancement: 13
  • Phenotypic Suppression: 9
  • Positive Genetic: 6
  • Synthetic Growth Defect: 20
  • Synthetic Haploinsufficiency: 1
  • Synthetic Lethality: 46
  • Synthetic Rescue: 16
Regulation Details


The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.

PAF1 encodes a component of the Polymerase-Associated Factor 1 (Paf1) complex (Paf1C). Other members of Paf1C include Cdc73p, Ctr9p, Leo1p, and Rtf1p. Paf1C is highly conserved throughout eukaryotes and participates in multiple aspects of RNA polymerase II (RNAPII) transcriptional regulation. Paf1c promotes RNAPII transcription elongation and transcription-coupled histone modifications, thereby affecting various cellular processes such as gene expression, silencing, RNA maturation, DNA repair, and cell cycle progression. Paf1p functions as a scaffold for Paf1C, and is required for H2B K123 monoubiquitylation and the downstream di- and trimethylation of H3K4 and K79. Paf1p promotes H2B monoubiquitylation by facilitating association of ubiquitin-conjugating enzyme Rad6p with RNAPII during transcription elongation. Paf1p is also required for trimethylation of H3K36, and may function to reduce cryptic initiation and histone acetylation at 3' coding regions. Paf1C associates with RNAPII and influences the phosphorylation state of the RNAPII CTD. Paf1C functions cooperatively with other factors influencing chromatin structure, such as the elongation complex Spt4p-Spt5p, the histone chaperone FACT, and the chromatin remodeler Chd1p. Paf1C also coordinates transcription elongation with transcription termination and RNA 3'-end processing by recruiting 3'-end processing factors to chromatin.
Expression Details


Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.

Summary Paragraph

A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.

Last Updated: 2004-06-19

Literature Details


All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.