RRN3 / YKL125W Overview


Standard Name
RRN3 1
Systematic Name
YKL125W
SGD ID
SGD:S000001608
Feature Type
ORF , Verified
Description
Protein required for transcription of rDNA by RNA polymerase I; transcription factor independent of DNA template; involved in recruitment of RNA polymerase I to rDNA; structure reveals unique HEAT repeat fold and a surface serine patch; phosphorylation of serine patch impairs cell growth and reduces RNA polymerase I binding in vitro and RNA polymerase I recruitment to the rDNA gene in vivo 2 3 4
Name Description
Regulation of RNA polymerase I 1
Comparative Info
Sequence Details

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.


Protein Details

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.)
627
Mol. Weight (Da)
72346.9
Isoelectric Point
4.34
Median Abundance (molecules/cell)
334 +/- 279
Half-life (hr)
1.7

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. Click "YeastMine" to view all alleles in YeastMine.


View all RRN3 alleles in SGD search | YeastMine

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.


Summary
rDNA-binding RNA polymerase I transcription factor involved in the assembly of the RNA polymerase I preinitiation complex (PIC) and subsequence synthesis of the nuclear large rRNA transcript; localized to the nucleolus

View computational annotations

Biological Process

Manually Curated

Cellular Component

Manually Curated
Phenotype Details

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.


Interaction Details

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.


191 total interactions for 159 unique genes

Physical Interactions

  • Affinity Capture-MS: 5
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 9
  • Co-crystal Structure: 8
  • Co-localization: 2
  • Co-purification: 3
  • Reconstituted Complex: 5
  • Two-hybrid: 1

Genetic Interactions

  • Dosage Rescue: 2
  • Negative Genetic: 136
  • Phenotypic Enhancement: 1
  • Phenotypic Suppression: 1
  • Positive Genetic: 3
  • Synthetic Growth Defect: 2
  • Synthetic Lethality: 7
  • Synthetic Rescue: 3
Regulation Details

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
RRN3 encodes an evolutionarily-conserved basal transcription factor required for RNA polymerase I (Pol I) transcription initiation. Rrn3p contains a tandem array of HEAT repeats that are on average approximately 40 residues long, encompassing the entire length of Rrn3p. These repeats fold into an elongated and bent conformation that wraps around Pol I. Rrn3p functions as a monomer and its association with Pol I is required to render the polymerase competent for transcription initiation. The level of the initiation competent Rrn3p-Pol I complex likely serves as a key regulatory process affecting the rate of rDNA synthesis in response to nutrient availability. Rrn3p-bound Pol I is recruited to rDNA promoters by the Pol I core factor (CF) complex through interactions between Rrn3p and the CF subunit Rrn6p.
Regulators
3
Targets
0
Expression Details

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 Details

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.


Primary
28
Additional
40
Reviews
28

Resources