RTF1 / YGL244W Overview
- Standard Name
- RTF1 1
- Systematic Name
- YGL244W
- SGD ID
- SGD:S000003213
- Aliases
- CSL3 6
- Feature Type
- ORF , Verified
- Description
- Subunit of RNAPII-associated chromatin remodeling Paf1 complex; regulates gene expression by directing cotranscriptional histone modification, influences transcription and chromatin structure through several independent functional domains; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in transcription elongation as demonstrated by the G-less-based run-on (GLRO) assay 1 2 3 4 5
- Name Description
- Restores TBP Function 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.
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.
- Length (a.a.)
- 558
- Mol. Weight (Da)
- 65849.3
- Isoelectric Point
- 5.02
- Median Abundance (molecules/cell)
- 6510 +/- 1376
- Half-life (hr)
- 4.9
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 RTF1 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; involved in regulation of transcription from RNA Pol I and II promoters, snoRNA 3'-end processing, regulation of histone H2B ubiquitination and H3 methylation and other cellular processes
View computational annotations
Molecular Function
- Manually Curated
- enables RNA binding (IDA)
- enables RNA polymerase II C-terminal domain phosphoserine binding (IDA)
Biological Process
- Manually Curated
- involved in DNA-templated transcription termination (IMP)
- involved in global genome nucleotide-excision repair (IMP)
- involved in meiotic DNA double-strand break formation (IMP)
- involved in mRNA 3'-end processing (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 regulation of transcription by RNA polymerase II (IGI)
- involved in regulation of transcription-coupled nucleotide-excision repair (IGI)
- involved in sno(s)RNA 3'-end processing (IMP)
- involved in sno(s)RNA transcription (IMP)
- involved in snoRNA transcription by RNA polymerase II (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.
Classical Genetics
- null
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- competitive fitness: decreased
- desiccation resistance: decreased
- haploproficient
- heat sensitivity: increased
- innate thermotolerance: decreased
- killer toxin resistance: decreased
- liquid culture appearance: abnormal
- metal resistance: decreased
- protein/peptide accumulation: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: absent
- respiratory growth: decreased
- sporulation efficiency: decreased
- sporulation: decreased
- stress resistance: decreased
- telomere length: decreased
- transposable element transposition: decreased
- transposable element transposition: increased
- UV resistance: decreased
- vegetative growth: decreased
- vegetative growth: decreased rate
- viable
Large-scale Survey
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.
1270 total interactions for 750 unique genes
Physical Interactions
- Affinity Capture-MS: 107
- Affinity Capture-RNA: 3
- Affinity Capture-Western: 36
- Biochemical Activity: 2
- Co-fractionation: 1
- Co-localization: 3
- Co-purification: 1
- Protein-RNA: 4
- Reconstituted Complex: 11
- Two-hybrid: 6
Genetic Interactions
- Dosage Growth Defect: 1
- Dosage Lethality: 2
- Dosage Rescue: 6
- Negative Genetic: 777
- Phenotypic Enhancement: 5
- Phenotypic Suppression: 10
- Positive Genetic: 143
- Synthetic Growth Defect: 75
- Synthetic Lethality: 62
- Synthetic Rescue: 15
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
- RTF1 encodes a component of the Polymerase-Associated Factor 1 (Paf1) complex (Paf1C). Other members of Paf1C include Cdc73p, Ctr9p, Leo1p, and Paf1p. 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. Within Paf1C, Rtf1p plays a key role in recruiting the complex to chromatin. Important for recruitment is its central Plus3 domain, also termed the ORF Association Region (OAR). Rtf1p also contains in its N-terminus a recruitment domain for the ATP-dependent chromatin remodeling factor Chd1p and a histone modification domain. Its C-terminus contains an interaction domain required for the association of Rtf1p with other Paf1C subunits. Rtf1p is primarily responsible for the monoubiquitylation of histone H2B K123 by enhancing recruitment of the ubiquitin-conjugating enzyme Rad6p and the ubiquitin protein ligase Bre1p to chromatin. Paf1C thereby influences gene expression by promoting histone H2BK123 ubiquitylation and subsequent methylation at histone H3K4 and K79 by the Set1p and Dot1p methyltransferases, respectively. Paf1C associates with RNAPII and influences the phosphorylation state of the RNAPII CTD. Paf1C promotes histone H3K36 trimethylation and affects histone acetylation levels. Paf1C functions cooperatively with other factors influencing chromatin structure, such as the elongation complex Spt4p-Spt5p, and the histone chaperone FACT. Paf1C also coordinates transcription elongation with transcription termination and RNA 3'-end processing.
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.
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.