UME6 / YDR207C Overview
- Standard Name
- UME6 1
- Systematic Name
- YDR207C
- SGD ID
- SGD:S000002615
- Aliases
- CAR80 1 2 , NIM2 , RIM16 25
- Feature Type
- ORF , Verified
- Description
- Rpd3L histone deacetylase complex subunit; key transcriptional regulator of early meiotic genes; involved in chromatin remodeling and transcriptional repression via DNA looping; binds URS1 upstream regulatory sequence, represses transcription by recruiting conserved histone deacetylase Rpd3p (through co-repressor Sin3p) and chromatin-remodeling factor Isw2p; couples metabolic responses to nutritional cues with initiation and progression of meiosis 2 3 4 5 6 7 8 9 11 12 13
- Name Description
- Unscheduled Meiotic gene Expression 10
- 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.)
- 836
- Mol. Weight (Da)
- 91154.5
- Isoelectric Point
- 10.11
- Median Abundance (molecules/cell)
- 1199 +/- 740
- Half-life (hr)
- 10.2
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 UME6 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
- Sequence-specific DNA-binding transcription factor involved in chromatin remodeling as it relates to the regulation of pseudohyphal growth, mitosis, meiosis, sporulation, lipid metabolism and nitrogen catabolite repression; component of the Rpd3L histone deacetylase complex
View computational annotations
Molecular Function
- Manually Curated
- enables DNA-binding transcription factor binding (IPI, IDA)
- enables DNA-binding transcription repressor activity, RNA polymerase II-specific (IDA, IMP)
- enables RNA polymerase II cis-regulatory region sequence-specific DNA binding (IDA)
- enables sequence-specific DNA binding (HDA)
- enables zinc ion binding (RCA)
Biological Process
- Manually Curated
- involved in cellular response to nitrogen starvation (IMP)
- involved in chromatin remodeling (IMP)
- involved in lipid droplet organization (IMP)
- involved in meiotic cell cycle (IMP)
- involved in mitotic cell cycle (IMP)
- involved in negative regulation of inositol biosynthetic process (IMP)
- involved in negative regulation of transcription by RNA polymerase II (IMP)
- involved in positive regulation of phosphatidylcholine biosynthetic process (IMP)
- involved in positive regulation of phosphatidylserine biosynthetic process (IMP)
- involved in positive regulation of transcription by RNA polymerase II (IMP)
- involved in pseudohyphal growth (IMP)
- involved in spore germination (IMP)
Cellular Component
- Manually Curated
- part of Rpd3L complex (IDA, HDA)
- part of Rpd3L-Expanded complex (HDA)
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
- Non-essential gene; null mutant glows slowly, has decreased ethanol tolerance, abnormal morphology of vacuoles and lipid particles, shortened lifespan, and is sensitive to DNA-damaging agents, caffeine, metals, heat, osmotic stress, desiccation, antimalarial quinine, and TOR inhibitor rapamycin; diploid mutants are defective in sporulation
Classical Genetics
- null
- chemical compound accumulation: decreased
- chemical compound excretion: increased
- chromosome/plasmid maintenance: decreased rate
- lipid particle morphology: abnormal
- metal resistance: decreased
- mitotic recombination: increased rate
- mutation frequency: increased rate
- protein/peptide accumulation: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- spore germination: absent
- spore germination: decreased
- vacuolar transport: decreased
- unspecified
- null
- alkaline pH resistance: decreased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- chitin deposition: increased
- chronological lifespan: decreased
- competitive fitness: decreased
- desiccation resistance: decreased
- endocytosis: decreased
- heat sensitivity: increased
- hyperosmotic stress resistance: decreased
- innate thermotolerance: decreased
- metal resistance: decreased
- oxidative stress resistance: decreased
- protein/peptide accumulation: increased
- protein/peptide distribution: abnormal
- resistance to chemicals: decreased
- resistance to chemicals: increased
- resistance to enzymatic treatment: decreased
- respiratory growth: absent
- size of nucleolus: increased
- sporulation efficiency: decreased
- sporulation: absent
- stress resistance: decreased
- toxin resistance: increased
- utilization of carbon source: decreased
- utilization of nitrogen source: decreased rate
- UV resistance: decreased
- vacuolar morphology: abnormal
- 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.
1689 total interactions for 1076 unique genes
Physical Interactions
- Affinity Capture-MS: 43
- Affinity Capture-RNA: 7
- Affinity Capture-Western: 7
- Biochemical Activity: 10
- Co-localization: 2
- Co-purification: 1
- Cross-Linking-MS (XL-MS): 1
- Proximity Label-MS: 245
- Reconstituted Complex: 6
- Two-hybrid: 15
Genetic Interactions
- Dosage Lethality: 2
- Dosage Rescue: 3
- Negative Genetic: 837
- Phenotypic Enhancement: 8
- Phenotypic Suppression: 9
- Positive Genetic: 203
- Synthetic Growth Defect: 25
- Synthetic Lethality: 171
- Synthetic Rescue: 94
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
- UME6 encodes a transcription factor that is a member of the C6 zinc finger class, containing a DNA binding domain also known as the Zn2Cys6 binuclear zinc cluster or zinc knuckle. Ume6p is a key regulator of meiosis and sporulation, repressing early meiosis-specific promoters during vegetative growth by binding to upstream repression sequences (URS1) and recruiting the Rpd3p-Sin3p histone deacetylase complex and the Isw2 chromatin remodeling complex. An important target of repression is NDT80, encoding a transcriptional activator that is central to establishing the commitment to meiosis. Ume6p has both positive and negative regulatory targets among genes involved in carbon and nitrogen metabolism, and may help to coordinate metabolic activity with meiosis. It is also involved in control of the induction of autophagy, via repression of ATG8 transcription. Transcriptional repression by Ume6p during vegetative growth is lifted by Ume6p degradation. In a two-step process, about 50% of Ume6p is destroyed after the transition to nonfermentable carbon sources, in a process that requires Ume6p acetylation by the SAGA acetyltransferase complex. In the absence of a nitrogen source during early meiosis, the remaining Ume6p interacts with the Ime1p transcription factor to trigger its complete destruction.
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: 2002-04-01
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.