CLN3/YAL040C Summary Help

Standard Name CLN3 1
Systematic Name YAL040C
Alias DAF1 2 , FUN10 3 , WHI1 4
Feature Type ORF, Verified
Description G1 cyclin involved in cell cycle progression; activates Cdc28p kinase to promote the G1 to S phase transition; plays a role in regulating transcription of the other G1 cyclins, CLN1 and CLN2; regulated by phosphorylation and proteolysis; acetly-CoA induces CLN3 transcription in response to nutrient repletion to promote cell-cycle entry. (4, 5, 6, 7 and see Summary Paragraph)
Name Description CycLiN
Chromosomal Location
ChrI:67520 to 65778 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -56 cM
Gene Ontology Annotations All CLN3 GO evidence and references
  View Computational GO annotations for CLN3
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 11 genes
Classical genetics
Large-scale survey
262 total interaction(s) for 165 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 4
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 14
  • Biochemical Activity: 6
  • PCA: 1
  • Protein-RNA: 1
  • Two-hybrid: 2

Genetic Interactions
  • Dosage Growth Defect: 4
  • Dosage Lethality: 3
  • Dosage Rescue: 17
  • Negative Genetic: 84
  • Phenotypic Enhancement: 25
  • Phenotypic Suppression: 16
  • Positive Genetic: 28
  • Synthetic Growth Defect: 13
  • Synthetic Lethality: 18
  • Synthetic Rescue: 23

Expression Summary
Length (a.a.) 580
Molecular Weight (Da) 64,990
Isoelectric Point (pI) 9.78
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrI:67520 to 65778 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -56 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1743 67520..65778 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000038

CLN3 encodes a G1 cyclin involved in regulation of the cell cycle. Progression through the cell cycle is a carefully regulated process that is conserved throughout eukaryotes. Periodic activation of cyclin-dependent kinases (CDKs) are required for this process; the critical CDK involved in cell cycle progression in yeast is Cdc28p.

Cyclins are the regulatory subunits that activate CDKs at the appropriate time in the cell cycle; they were named for their cyclical accumulation during particular phases of the cell cycle (8). Distinct CDK-cyclin complexes are required for progression through different stages of the cell cycle (9). CLN1, CLN2, and CLN3 encode the yeast cyclins involved in the G1 to S phase transition.

While transcription of CLN1 and CLN2 is regulated by the cell cycle, CLN3 transcription is not. Instead, Cln3p is regulated post-translationally (6, 5). Cln3p is an unstable protein that contains several PEST motifs, which are sequences rich in proline, glutamic acid, serine, and threonine and are found in many other unstable proteins (6, 5). Cln3p is phosphorylated by Cdc28p; this phosphorylation may make the Cln3 protein less stable (5). The chaperone Ydj1p is required for the phosphorylation and degradation of Cln3p (10). In addition to being carefully regulated itself, Cln3p also plays a role in regulating the transcriptional activation of the other G1 cyclins, CLN1 and CLN2 (11, 12). An excellent review by Lew et al. describes cell cycle control in S. cerevisiae in detail (9).

Last updated: 1999-12-17 Contact SGD

References cited on this page View Complete Literature Guide for CLN3
1) Tokiwa, G.  (1992) Personal Communication, Mortimer Map Edition 11
2) Cross FR  (1988) DAF1, a mutant gene affecting size control, pheromone arrest, and cell cycle kinetics of Saccharomyces cerevisiae. Mol Cell Biol 8(11):4675-84
3) Coleman KG, et al.  (1986) Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: isolation and characterization of the CDC24 gene and adjacent regions of the chromosome. Mol Cell Biol 6(12):4516-25
4) Nash R, et al.  (1988) The WHI1+ gene of Saccharomyces cerevisiae tethers cell division to cell size and is a cyclin homolog. EMBO J 7(13):4335-46
5) Cross FR and Blake CM  (1993) The yeast Cln3 protein is an unstable activator of Cdc28. Mol Cell Biol 13(6):3266-71
6) Tyers M, et al.  (1992) The Cln3-Cdc28 kinase complex of S. cerevisiae is regulated by proteolysis and phosphorylation. EMBO J 11(5):1773-84
7) Shi L and Tu BP  (2013) Acetyl-CoA induces transcription of the key G1 cyclin CLN3 to promote entry into the cell division cycle in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 110(18):7318-23
8) Evans T, et al.  (1983) Cyclin: a protein specified by maternal mRNA in sea urchin eggs that is destroyed at each cleavage division. Cell 33(2):389-96
9) Lew DJ, et al.  (1997) "Cell cycle control in Saccharomyces cerevisiae." Pp. 607-695 in The Molecular and Cellular Biology of the Yeast Saccharomyces: Cell Cycle and Cell Biology, edited by Pringle JR, Broach JR and Jones EW. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
10) Yaglom JA, et al.  (1996) The molecular chaperone Ydj1 is required for the p34CDC28-dependent phosphorylation of the cyclin Cln3 that signals its degradation. Mol Cell Biol 16(7):3679-84
11) Stuart D and Wittenberg C  (1995) CLN3, not positive feedback, determines the timing of CLN2 transcription in cycling cells. Genes Dev 9(22):2780-94
12) Dirick L, et al.  (1995) Roles and regulation of Cln-Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. EMBO J 14(19):4803-13