PAF1 / YBR279W Overview
- Standard Name
- PAF1 1
- Systematic Name
- YBR279W
- SGD ID
- SGD:S000000483
- 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
- Name Description
- RNA Polymerase II Associated Factor 1
- Comparative Info
-
Sequence
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.
- Summary
- PAF1/YBR279W is located on the right arm of chromosome II between DPB3 DNA polymerase epsilon subunit and SAF1 F-Box protein; coding sequence is 1338 nucleotides long with 16 synonymous SNPs and an in-frame 18-nucleotide duplication in strains SK1 and W303 after T1227
Analyze Sequence
S288C only
BLASTN | BLASTP | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes | Six-Frame Translation
S288C vs. other species
BLASTN vs. fungi | BLASTP at NCBI | BLASTP vs. fungi
S288C vs. other strains
Protein
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.
- Summary
- Paf1p is 445 amino acids long, shorter-lived, low in abundance; contains disordered region at C-terminus; acetylated on 3 lysines, sumoylated on 4 lysines, phosphorylated on 17 residues; strains SK1 and W303 have a 6 amino acid duplication ENKQDE between Glu410 and Glu411
- Length (a.a.)
- 445
- Mol. Weight (Da)
- 51771.2
- Isoelectric Point
- 4.54
- Median Abundance (molecules/cell)
- 5232 +/- 1675
- Half-life (hr)
- 8.6
Alleles
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
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.
- Summary
- 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
Molecular Function
- Manually Curated
- enables chromatin binding (IDA)
- enables RNA polymerase II C-terminal domain phosphoserine binding (IDA)
- enables RNA polymerase II complex binding (IPI)
Biological Process
- Manually Curated
- involved in DNA-templated transcription termination (IMP)
- involved in G1/S transition of mitotic cell cycle (IMP)
- involved in global genome nucleotide-excision repair (IMP)
- involved in mRNA 3'-end processing (IMP)
- involved in negative regulation of DNA recombination (IMP)
- involved in negative regulation of mitophagy (IMP)
- involved in negative regulation of transcription by RNA polymerase II (IMP)
- involved in positive regulation of transcription elongation by RNA polymerase I (IDA)
- involved in positive regulation of transcription elongation by RNA polymerase II (IMP)
- involved in rDNA heterochromatin formation (IMP)
- involved in regulation of transcription by RNA polymerase II (IMP)
- involved in regulation of transcription-coupled nucleotide-excision repair (IGI)
- involved in rRNA processing (IMP)
- involved in sno(s)RNA 3'-end processing (IMP)
- involved in sno(s)RNA transcription (IMP)
- involved in snoRNA transcription by RNA polymerase II (IDA, IMP)
- involved in transcription by RNA polymerase I (IGI, IMP)
- involved in transcription by RNA polymerase III (IMP)
- involved in transcription elongation by RNA polymerase I (IMP)
- involved in transcription elongation by RNA polymerase II (IGI, IMP)
Cellular Component
- Manually Curated
- part of Cdc73/Paf1 complex (IPI)
- located in euchromatin (IDA)
- located in nucleus (IDA)
Complex
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
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.
- Summary
- PAF1/YBR279W is a non-essential gene, null mutants are viable and associated with a variety of phenotypes that significantly impact cellular functions and overall fitness. Mutants lacking PAF1 exhibit a decreased rate of anaerobic growth, indicating a compromised ability to thrive in low-oxygen environments. These mutants display abnormal bud morphology and experience delays in cell cycle progression during the G1 phase, which can hinder normal cell division. Cell size is increased, yet the chronological lifespan is decreased, suggesting a trade-off between growth and longevity. Cold sensitivity is heightened, making these mutants more vulnerable to lower temperatures, while competitive fitness is diminished, leading to reduced viability in resource-limited conditions. Resistance to desiccation, hydrostatic pressure, and killer toxins is decreased, further underscoring their compromised resilience. The growth rate during the exponential phase is also reduced, and heat sensitivity is increased, indicating greater susceptibility to elevated temperatures. Although oxidative stress resistance is increased, the replicative lifespan is extended, which may reflect a complex relationship between stress responses and cellular aging. However, the mutants show an absent mating response and sporulation, indicating disruptions in reproductive capabilities. Metal resistance is decreased, and the morphology of lipid particles is abnormal, which could affect cellular metabolism. Telomere length is reduced, and transposable element transposition is increased, suggesting potential genomic instability. Vacuolar morphology is also abnormal, impacting cellular storage and waste management. Overexpression of PAF1 decreases growth rate during the exponential phase, highlighting the gene's intricate role in regulating growth and cellular processes.
Classical Genetics
- null
- anaerobic growth: decreased rate
- auxotrophy
- chemical compound accumulation: increased
- chronological lifespan: decreased
- cold sensitivity: increased
- growth in exponential phase: decreased rate
- heat sensitivity: increased
- metal resistance: decreased
- protein secretion: decreased
- protein/peptide accumulation: increased
- protein/peptide modification: increased
- replicative lifespan: increased
- resistance to chemicals: decreased
- respiratory growth: decreased rate
- RNA accumulation: decreased
- vacuolar morphology: abnormal
- vegetative growth: decreased
- vegetative growth: normal
- overexpression
- null
- bud morphology: abnormal
- cell cycle progression in G1 phase: delayed
- cell size: increased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- chronological lifespan: decreased
- cold sensitivity: increased
- competitive fitness: decreased
- desiccation resistance: decreased
- haploinsufficient
- haploproficient
- heat sensitivity: increased
- hydrostatic pressure resistance: decreased
- innate thermotolerance: decreased
- killer toxin resistance: decreased
- lipid particle morphology: abnormal
- mating response: absent
- metal resistance: decreased
- oxidative stress resistance: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: decreased
- sporulation: absent
- telomere length: decreased
- toxin resistance: decreased
- toxin resistance: increased
- transposable element transposition: increased
- utilization of carbon source: decreased rate
- vacuolar morphology: abnormal
- vegetative growth: decreased rate
- viable
Large-scale Survey
Disease
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.
- Summary
- Yeast PAF1 is homologous to human PAF1, and has been used to study pancreatic oncogenesis
Manually Curated
Interaction
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.
- Summary
- Paf1p interacts physically with proteins involved in transcription; PAF1 interacts genetically with genes involved in transcription
373 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: 10
- Positive Genetic: 6
- Synthetic Growth Defect: 20
- Synthetic Haploinsufficiency: 1
- Synthetic Lethality: 46
- Synthetic Rescue: 16
Regulation
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.
- Summary
- 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
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
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.