The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
CAF120 (systematic name YNL278W) encodes a 120 kDa CCR4-associated factor in Saccharomyces cerevisiae (baker's yeast). The protein was originally identified by its physical association with the CCR4 protein, the major cytoplasmic mRNA deadenylase in yeast (goldstrohm2007pufproteinmediateddeadenylation pages 1-2). CAF120 is a member of the CAF120 protein family and contains Pleckstrin Homology (PH)-like domains (InterPro: IPR011993, IPR001849, IPR058155), which typically function as protein-protein or protein-lipid interaction modules. It is important to note that CAF120 is distinct from Caf130, another yeast-specific CCR4-associated factor that is consistently listed as a core subunit of the CCR4-NOT complex.
The key properties of CAF120 are summarized in the following table:
| Property | Summary |
|---|---|
| Protein name | CCR4-NOT transcriptional complex subunit CAF120; also described as a 120 kDa CCR4-associated factor (goldstrohm2007pufproteinmediateddeadenylation pages 1-2, hagkarim2020theregulatoryproperties pages 1-3) |
| Gene name | CAF120 (goldstrohm2007pufproteinmediateddeadenylation pages 1-2) |
| Systematic name | YNL278W (goldstrohm2007pufproteinmediateddeadenylation pages 1-2, kim2018globalanalysisof pages 75-77) |
| Organism | Saccharomyces cerevisiae (baker’s yeast; strain S288C/background strains used in cited studies) (goldstrohm2007pufproteinmediateddeadenylation pages 1-2, philipp2019networkrewiringof pages 1-3) |
| Molecular weight | ~120 kDa by nomenclature/original factor description; exact mass not established in the cited papers here (goldstrohm2007pufproteinmediateddeadenylation pages 1-2, hagkarim2020theregulatoryproperties pages 1-3) |
| Domain architecture | Contains PH/PH-like domains per UniProt/domain annotations supplied in the research prompt; consistent with a likely non-catalytic scaffolding or interaction role, but no primary structural study for yeast Caf120 was identified here (supported functionally by lack of known catalytic activity) (philipp2019networkrewiringof pages 7-8, hagkarim2020theregulatoryproperties pages 1-3) |
| Known functions | Non-catalytic CCR4-associated factor linked to the broader CCR4-NOT gene-expression machinery; not required for HO mRNA deadenylation in the tested assay, but contributes to normal meiotic crossover frequency, implicating it in meiotic recombination/crossover control (goldstrohm2007pufproteinmediateddeadenylation pages 2-3, philipp2019networkrewiringof pages 7-8) |
| Subcellular localization | Detected at the cytoplasm, bud neck, and bud in a proteome-scale localization/homomerization study (kim2018globalanalysisof pages 75-77) |
| Deletion phenotype | caf120Δ showed no apparent effect on HO mRNA poly(A) tail length/deadenylation in the Mpt5p/HO assay; in contrast, caf120Δ reduced meiotic genetic distance/crossover frequency in the CEN8-THR1 interval assay (goldstrohm2007pufproteinmediateddeadenylation pages 2-3, philipp2019networkrewiringof pages 7-8) |
| Key interactors / pathway context | Functionally associated with the CCR4-NOT/CCR4-Pop2-Not complex context in mRNA regulation; genetically/functionally linked to the MutLγ-Exo1 meiotic crossover pathway, where Caf120 emerged from a screen of metaphase I-enriched interactors affecting crossover formation (goldstrohm2007pufproteinmediateddeadenylation pages 1-2, philipp2019networkrewiringof pages 7-8, philipp2019networkrewiringof pages 8-9) |
| Essential gene? | Non-essential under standard laboratory conditions; viable deletion strains were used in both deadenylation and meiotic crossover studies (goldstrohm2007pufproteinmediateddeadenylation pages 1-2, philipp2019networkrewiringof pages 7-8) |
Table: This table summarizes the main curated properties of yeast CAF120/YNL278W, including identity, localization, pathway context, and experimentally observed deletion phenotypes. It is useful as a compact reference because the literature on this specific protein is limited and dispersed across CCR4-NOT and meiosis studies.
The CCR4-NOT complex is a highly conserved, multisubunit assembly central to the regulation of eukaryotic gene expression. In S. cerevisiae, the complex was originally identified through genetic screens for transcription regulators and was later shown to carry the major cytoplasmic mRNA deadenylase activity (miller2012ccr4notcomplexthe pages 1-2, collart2016theccr4‐notcomplex pages 1-2). The nine core subunits of the yeast CCR4-NOT complex are: Not1 (the scaffold), Not2, Not3, Not4, Not5, Caf1 (Pop2), Ccr4, Caf40, and Caf130 (caulier2025theccr4–notcomplex pages 2-3, hagkarim2020theregulatoryproperties pages 1-3, chapat2014novelrolesof pages 1-2, collart2017theccr4notcomplex pages 1-4). These are organized into functional modules—a deadenylase module (Ccr4 and Caf1), a ubiquitination module (Not4), the NOT module (Not2-Not3-Not5), the Caf40 module, and a fifth module comprising Caf130—all docked onto the Not1 scaffold protein (collart2017theccr4notcomplex pages 1-4).
CAF120 is not consistently listed among these nine canonical core subunits. Rather, it appears to be an associated or peripheral factor of the CCR4-NOT complex. The original biochemical purification of Ccr4-containing complexes identified several CCR4-associated factors, including Caf1, Caf40, Caf130, and CAF120, as proteins that co-purify with Ccr4 (goldstrohm2007pufproteinmediateddeadenylation pages 1-2). The larger (~1.9 MDa) version of the complex may additionally contain a combination of factors such as Dhh1, Dbf2, Caf4, Caf16, and Btt1, beyond the ~1.0 MDa core (miller2012ccr4notcomplexthe pages 1-2, bartlam2010thestructuralbasis pages 1-3). The precise stoichiometric relationship of CAF120 to the core complex remains poorly defined.
CAF120 has no known enzymatic activity. It does not possess deadenylase, ubiquitin ligase, or any other catalytic function. Its PH-like domains are characteristic of scaffold or adaptor proteins that mediate protein-protein interactions. This structural architecture suggests that CAF120 functions as a non-catalytic, structural or regulatory component within the broader CCR4-NOT interaction network.
Direct experimental testing of CAF120's role in mRNA deadenylation has been performed. Goldstrohm et al. (2007) examined the deadenylation of HO mRNA—a well-characterized target of PUF protein-mediated poly(A) tail shortening—in a panel of deletion strains lacking various CCR4-NOT complex components. Deletion of CAF120 (caf120Δ) had no apparent effect on HO mRNA poly(A) tail length, in contrast to the severe deadenylation defects observed in ccr4Δ and pop2Δ strains (goldstrohm2007pufproteinmediateddeadenylation pages 2-3). This result was consistent across multiple non-essential subunits: deletions of Caf130, Not3, and Not4 also did not significantly affect HO deadenylation (goldstrohm2007pufproteinmediateddeadenylation pages 2-3). Thus, CAF120 is dispensable for at least one well-characterized deadenylation pathway.
Perhaps the most striking functional finding for CAF120 emerged from a large-scale proteomic and genetic study of homologous recombination enzymes by Wild et al. (2019). This study used affinity purification–mass spectrometry to characterize the interaction network of seven recombination intermediate processing enzymes (RIPEs) during mitotic proliferation and meiosis in S. cerevisiae (philipp2019networkrewiringof pages 1-3). CAF120 was identified as a metaphase I-enriched interactor of the MutLγ-Exo1 complex—the endonuclease system responsible for generating the majority of meiotic crossovers (philipp2019networkrewiringof pages 7-8).
A functional screen of metaphase I-enriched interactors revealed that deletion of CAF120 (caf120Δ) caused a reproducible reduction in genetic distance at the CEN8-THR1 interval, a standard measure of crossover frequency (philipp2019networkrewiringof pages 7-8). This phenotype was milder than that observed for chd1Δ, which showed a crossover defect comparable to deletion of core crossover genes (MLH1, MLH3, or EXO1), but it nonetheless demonstrated a functional role for CAF120 in meiotic recombination (philipp2019networkrewiringof pages 7-8). The molecular mechanism by which CAF120 contributes to crossover formation remains unknown, but its identification as a context-specific interactor of the MutLγ-Exo1 pathway suggests it may serve a scaffolding or regulatory role during the resolution of meiotic recombination intermediates.
A global analysis of protein homomerization in S. cerevisiae detected CAF120 as a protein capable of self-interaction (kim2018globalanalysisof pages 75-77). This capacity for homomerization may be relevant to its scaffolding function, potentially allowing multimerization-dependent assembly of protein complexes.
In a proteome-wide study of protein homomerization and localization, CAF120 was detected in the cytoplasm, at the bud neck, and in the bud (kim2018globalanalysisof pages 75-77). This predominantly cytoplasmic localization is consistent with the known primary localization of the CCR4-NOT complex. The parent CCR4-NOT complex has been detected in both the cytoplasm and the nucleus (collart2016theccr4‐notcomplex pages 2-4, chapat2014novelrolesof pages 5-6). In yeast, CCR4-NOT components are present in the cytoplasm where they carry out mRNA deadenylation, and in processing bodies (P-bodies) which are cytoplasmic granules involved in mRNA decay and storage (chapat2014novelrolesof pages 5-6). The complex also has nuclear functions including roles in transcription regulation, mRNA export, and nuclear RNA quality control (miller2012ccr4notcomplexthe pages 1-2, miller2012ccr4notcomplexthe pages 11-12, miller2012ccr4notcomplexthe pages 9-11). During the cell cycle, the complex shows dynamic redistribution: it concentrates in the nucleus during G1 phase and redistributes to the cytoplasm during S phase (hagkarim2020theregulatoryproperties pages 14-16). Recent comprehensive reviews, however, emphasize that the best-supported functions of the CCR4-NOT complex are cytoplasmic—deadenylation, mRNA decay, and translational control—while direct evidence for nuclear transcriptional roles has been more elusive (caulier2025theccr4–notcomplex pages 7-8).
CAF120 is embedded within the broader CCR4-NOT complex, which is the major eukaryotic deadenylase complex responsible for shortening poly(A) tails on mRNAs (collart2016theccr4‐notcomplex pages 1-2, caulier2025theccr4–notcomplex pages 1-2). This complex regulates gene expression at multiple levels: transcription initiation and elongation, mRNA quality control and export, translational control, co-translational quality control, and mRNA decay (collart2016theccr4‐notcomplex pages 1-2, collart2017theccr4notcomplex pages 1-4). Although CAF120 itself is not required for the deadenylation reaction, its association with the complex places it within this central mRNA metabolism machinery.
CAF120 participates in the MutLγ-Exo1 meiotic crossover pathway (philipp2019networkrewiringof pages 1-3, philipp2019networkrewiringof pages 7-8). During meiosis, recombination intermediates (joint molecules containing Holliday junctions) are resolved by structure-selective nucleases and the MutLγ-Exo1 endonuclease to generate crossovers. The MutLγ complex (Mlh1-Mlh3) works with Exo1 to produce the majority of meiotic crossovers. CAF120 was identified as a meiosis-specific (metaphase I-enriched) component of this pathway's interaction network, and its deletion reduces crossover frequency (philipp2019networkrewiringof pages 7-8).
CAF120 contains PH (Pleckstrin Homology) and PH-like domains, belonging to the PH-like domain superfamily (IPR011993) and specifically to the Skg3/CAF120-like PH family (IPR058155). PH domains are versatile protein-protein and protein-lipid interaction modules found in diverse signaling and scaffold proteins. In the context of CAF120, these domains are likely to mediate its association with other proteins, potentially including components of the CCR4-NOT complex or the meiotic recombination machinery.
CAF120 is a member of the CAF120 family (per UniProt classification), which appears to be restricted to fungi. The protein has no obvious orthologs in metazoan organisms (caulier2025theccr4–notcomplex pages 2-3), paralleling the situation with Caf130, another yeast-specific CCR4-NOT associated factor that lacks identifiable homologs outside of yeast. The recent comprehensive review by Caulier et al. (2025) confirms that the CCR4-NOT complex composition varies across organisms, with a universally conserved core enriched by lineage-specific subunits such as Caf130 in S. cerevisiae (caulier2025theccr4–notcomplex pages 1-2, caulier2025theccr4–notcomplex pages 2-3).
CAF120 is a non-essential gene under standard laboratory conditions. Viable deletion strains have been constructed and used in multiple studies (goldstrohm2007pufproteinmediateddeadenylation pages 1-2, philipp2019networkrewiringof pages 7-8). The deletion of CAF120 does not display any readily identifiable growth phenotype on standard media, consistent with the observation that deletion of Caf40 or Caf130 similarly does not display obvious growth defects (collart2016theccr4‐notcomplex pages 2-4). However, mild sensitivity or resistance changes to various conditions may exist, as documented in the Saccharomyces Genome Database (collart2016theccr4‐notcomplex pages 2-4). The most notable phenotype of caf120Δ is the reduction in meiotic crossover frequency (philipp2019networkrewiringof pages 7-8).
Recent studies on the CCR4-NOT complex (2023–2025) have focused primarily on the roles of core subunits in co-translational quality control, codon optimality-dependent mRNA decay, and ribosome-associated functions. A landmark study by Zhu et al. (2024) revealed that specific tRNAs in the ribosomal P-site recruit the CCR4-NOT complex via CNOT3/Not5, directly linking translation efficiency to mRNA stability. Collart et al. (2024) reviewed the expanding roles of the CCR4-NOT complex in co-translational processes, including protein folding and organelle targeting. A comprehensive 2025 review by Caulier et al. in Nucleic Acids Research provided an updated evolutionary perspective on CCR4-NOT complex composition and function (caulier2025theccr4–notcomplex pages 1-2). However, no recent studies have specifically addressed the function or structure of CAF120 itself, leaving this protein as one of the less characterized components of the broader CCR4-NOT interaction network.
CAF120/YNL278W is a poorly characterized, non-catalytic, PH domain-containing protein associated with the CCR4-NOT complex in S. cerevisiae. While it was originally identified as a CCR4-associated factor, it is not required for the canonical deadenylation function of the complex. Its most clearly defined biological role is in meiotic crossing-over, where it contributes to normal crossover frequency through the MutLγ-Exo1 pathway. Its PH-like domains suggest a scaffolding or adapter function, potentially bridging protein-protein interactions within the CCR4-NOT complex or between the complex and other cellular machinery. Significant knowledge gaps remain regarding: (1) the precise structural basis for CAF120's interaction with the CCR4-NOT complex and its docking site on Not1; (2) the molecular mechanism by which it promotes meiotic crossover formation; (3) whether it has additional condition-specific functions beyond deadenylation and meiosis; and (4) the functional significance of its homomerization capacity and cytoplasmic/bud neck localization.
References
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(collart2016theccr4‐notcomplex pages 2-4): Martine A. Collart. The ccr4‐not complex is a key regulator of eukaryotic gene expression. Wiley Interdisciplinary Reviews. RNA, 7:438-454, Jan 2016. URL: https://doi.org/10.1002/wrna.1332, doi:10.1002/wrna.1332. This article has 446 citations and is from a peer-reviewed journal.
(chapat2014novelrolesof pages 5-6): Clément Chapat and Laura Corbo. Novel roles of the ccr4–not complex. Wiley Interdisciplinary Reviews: RNA, 5:883-901, Nov 2014. URL: https://doi.org/10.1002/wrna.1254, doi:10.1002/wrna.1254. This article has 33 citations.
(miller2012ccr4notcomplexthe pages 11-12): Jason E. Miller and Joseph C. Reese. Ccr4-not complex: the control freak of eukaryotic cells. Critical Reviews in Biochemistry and Molecular Biology, 47:315-333, Jun 2012. URL: https://doi.org/10.3109/10409238.2012.667214, doi:10.3109/10409238.2012.667214. This article has 222 citations and is from a peer-reviewed journal.
(miller2012ccr4notcomplexthe pages 9-11): Jason E. Miller and Joseph C. Reese. Ccr4-not complex: the control freak of eukaryotic cells. Critical Reviews in Biochemistry and Molecular Biology, 47:315-333, Jun 2012. URL: https://doi.org/10.3109/10409238.2012.667214, doi:10.3109/10409238.2012.667214. This article has 222 citations and is from a peer-reviewed journal.
(hagkarim2020theregulatoryproperties pages 14-16): Nafiseh Chalabi Hagkarim and Roger J. Grand. The regulatory properties of the ccr4–not complex. Cells, 9:2379, Oct 2020. URL: https://doi.org/10.3390/cells9112379, doi:10.3390/cells9112379. This article has 88 citations.
(caulier2025theccr4–notcomplex pages 7-8): Guillaume Caulier, Joseph Siblini, Lina Sène, Fabienne Mauxion, and Bertrand Séraphin. The ccr4–not complex: a multifaceted sensor of molecular signals instructing eukaryotic mrna translation and stability. Nucleic Acids Research, Nov 2025. URL: https://doi.org/10.1093/nar/gkaf1401, doi:10.1093/nar/gkaf1401. This article has 8 citations and is from a highest quality peer-reviewed journal.
(caulier2025theccr4–notcomplex pages 1-2): Guillaume Caulier, Joseph Siblini, Lina Sène, Fabienne Mauxion, and Bertrand Séraphin. The ccr4–not complex: a multifaceted sensor of molecular signals instructing eukaryotic mrna translation and stability. Nucleic Acids Research, Nov 2025. URL: https://doi.org/10.1093/nar/gkaf1401, doi:10.1093/nar/gkaf1401. This article has 8 citations and is from a highest quality peer-reviewed journal.