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protein coding gene - caf1 (SPCC18.06c) - CCR4-Not complex CAF1 family ribonuclease subunit 7/8

Gene summary

Standard name
caf1
Systematic ID
SPCC18.06c
Product
CCR4-Not complex CAF1 family ribonuclease subunit 7/8
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
pop2
UniProt ID
O74856
ORFeome ID
14/14F07
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome III: 1965430..1966906 reverse strand

Annotation

GO biological process

GO:0010629 - negative regulation of gene expression

References:

GO:0000289 - nuclear-transcribed mRNA poly(A) tail shortening

References:

GO:0031047 - regulatory ncRNA-mediated gene silencing

References:

GO cellular component

GO:0030014 - CCR4-NOT complex

References:

GO:0030015 - CCR4-NOT core complex

References:

GO:0005829 - cytosol

References:

GO:0000932 - P-body

References:

GO molecular function

GO:0003682 - chromatin binding

References:

GO:0030145 - manganese ion binding

References:

GO:0046872 - metal ion binding

References:

GO:0003729 - mRNA binding

References:

GO:0004535 - poly(A)-specific ribonuclease activity

References:

GO:0004540 - RNA nuclease activity

References:

GO:0008270 - zinc ion binding

References:

Modification

MOD:00046 - O-phospho-L-serine

References:

MOD:00047 - O-phospho-L-threonine

References:

Multi-locus phenotype

FYPO:0004745 - abolished histone H3-K9 dimethylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0006112 - abolished histone H3-K9 dimethylation at silent mating-type cassette during vegetative growth

References:

Genotypes:

FYPO:0006111 - abolished histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth

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Genotypes:

FYPO:0002820 - abolished histone H3-K9 methylation at telomere during vegetative growth

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Genotypes:

FYPO:0005738 - abolished histone H3-S10 phosphorylation during vegetative growth

References:

Genotypes:

FYPO:0002827 - decreased chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0004604 - decreased chromatin silencing at subtelomere

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0005917 - increased subtelomeric heterochromatin RNA level

References:

Genotypes:

FYPO:0002336 - normal chromatin silencing at silent mating-type cassette

References:

Genotypes:

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0000031 - abnormal mating

References:

Genotypes:

FYPO:0007336 - abolished chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0002926 - abolished poly(A) RNA binding

References:

Genotypes:

FYPO:0008056 - abolished poly(A)-specific ribonuclease activity

References:

Genotypes:

FYPO:0000080 - decreased cell population growth at low temperature

References:

Genotypes:

FYPO:0003743 - decreased cell population growth during glucose starvation

References:

Genotypes:

FYPO:0009078 - decreased cell population growth on ethanol carbon source

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Genotypes:

FYPO:0000684 - decreased cell population growth on glycerol carbon source

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Genotypes:

FYPO:0009091 - decreased cell population growth on lysine and proline nitrogen source

References:

Genotypes:

FYPO:0009092 - decreased cell population growth on lysine and serine nitrogen source

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Genotypes:

FYPO:0007562 - decreased cell population growth on serine nitrogen source

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Genotypes:

FYPO:0009097 - decreased cell population growth on xylose carbon source

References:

Genotypes:

FYPO:0006993 - decreased chromatin silencing at centromere otr1R

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Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

References:

Genotypes:

FYPO:0002827 - decreased chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0004604 - decreased chromatin silencing at subtelomere

References:

Genotypes:

FYPO:0002355 - decreased histone H3-K9 dimethylation at silent mating-type cassette during vegetative growth

References:

Genotypes:

FYPO:0004137 - decreased histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth

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Genotypes:

FYPO:0005845 - decreased histone H3-K9 trimethylation at silent mating-type cassette during vegetative growth

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Genotypes:

FYPO:0000708 - decreased mating efficiency

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Genotypes:

FYPO:0003573 - decreased protein localization to heterochromatin at silent mating-type cassette

References:

Genotypes:

FYPO:0007891 - decreased spatial extent of mating-type region heterochromatin assembly

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Genotypes:

FYPO:0007480 - decreased spatial extent of subtelomeric heterochromatin assembly

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Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0005258 - increased cell population growth at high temperature

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Genotypes:

FYPO:0009095 - increased cell population growth on fructose carbon source

References:

Genotypes:

FYPO:0005261 - increased cell population growth on galactose carbon source

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Genotypes:

FYPO:0009052 - increased cell population growth on glutamate nitrogen source

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Genotypes:

FYPO:0009098 - increased cell population growth on mannitol carbon source

References:

Genotypes:

FYPO:0009076 - increased cell population growth on sucrose carbon source

References:

Genotypes:

FYPO:0006926 - increased nucleus:cytoplasm ratio

References:

Genotypes:

FYPO:0008058 - increased polyA ribonuclease processivity

References:

Genotypes:

FYPO:0001551 - increased protein level during cellular response to zinc ion starvation

References:

Genotypes:

FYPO:0004377 - increased protein localization to heterochromatin at silent mating-type cassette

References:

Genotypes:

FYPO:0005291 - increased RNA level during cellular response to zinc ion

References:

Genotypes:

FYPO:0001547 - increased RNA level during cellular response to zinc ion starvation

References:

Genotypes:

FYPO:0006110 - increased silent mating-type cassette transcript-derived siRNA level

References:

Genotypes:

FYPO:0006109 - increased subtelomeric transcript-derived siRNA level

References:

Genotypes:

FYPO:0004557 - increased vegetative cell population growth

References:

Genotypes:

FYPO:0006518 - loss of viability in G0

References:

Genotypes:

FYPO:0007553 - normal G1 to G0 transition

References:

Genotypes:

FYPO:0007035 - normal growth on 5-fluorouracil

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Genotypes:

FYPO:0008442 - normal growth on ethylenediaminetetraacetic acid

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Genotypes:

FYPO:0003507 - normal growth on zinc

References:

Genotypes:

FYPO:0004083 - normal protein level

References:

Genotypes:

FYPO:0008441 - normal protein level during cellular response to replete zinc

References:

Genotypes:

FYPO:0007054 - normal protein level during cellular response to zinc ion starvation

References:

Genotypes:

FYPO:0004378 - normal protein localization to heterochromatin at silent mating-type cassette

References:

Genotypes:

FYPO:0002357 - normal protein-RNA interaction

References:

Genotypes:

FYPO:0006829 - normal RNA level during cellular response to zinc ion starvation

References:

Genotypes:

FYPO:0009041 - resistance to 2,2′-dipyridyl

References:

Genotypes:

FYPO:0009030 - resistance to amitrole

References:

Genotypes:

FYPO:0009031 - resistance to bleomycin

References:

Genotypes:

FYPO:0000067 - resistance to brefeldin A

References:

Genotypes:

FYPO:0000763 - resistance to cadmium

References:

Genotypes:

FYPO:0009068 - resistance to ciclopirox olamine

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Genotypes:

FYPO:0002634 - resistance to cobalt

References:

Genotypes:

FYPO:0000764 - resistance to cycloheximide

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Genotypes:

FYPO:0009034 - resistance to ethylenediaminetetraacetic acid

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Genotypes:

FYPO:0009070 - resistance to itraconazole

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Genotypes:

FYPO:0001583 - resistance to lithium

References:

Genotypes:

FYPO:0009083 - resistance to lithium chloride and methyl methanesulfonate

References:

Genotypes:

FYPO:0000725 - resistance to methyl methanesulfonate

References:

Genotypes:

FYPO:0009043 - resistance to potassium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0005968 - resistance to sodium chloride

References:

Genotypes:

FYPO:0005266 - resistance to sodium dodecyl sulfate

References:

Genotypes:

FYPO:0002767 - resistance to terbinafine

References:

Genotypes:

FYPO:0003383 - resistance to tert-butyl hydroperoxide

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Genotypes:

FYPO:0000830 - resistance to vanadate

References:

Genotypes:

FYPO:0001098 - sensitive to 4-nitroquinoline N-oxide

References:

Genotypes:

FYPO:0009067 - sensitive to amorolfine

References:

Genotypes:

FYPO:0002642 - sensitive to amphotericin B

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Genotypes:

FYPO:0001701 - sensitive to bortezomib

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Genotypes:

FYPO:0000096 - sensitive to cadmium

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Genotypes:

FYPO:0000097 - sensitive to caffeine during vegetative growth

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Genotypes:

FYPO:0000098 - sensitive to calcium

References:

Genotypes:

FYPO:0001188 - sensitive to Calcofluor White

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Genotypes:

FYPO:0000085 - sensitive to camptothecin

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Genotypes:

FYPO:0001245 - sensitive to cobalt

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Genotypes:

FYPO:0000104 - sensitive to cycloheximide

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Genotypes:

FYPO:0003559 - sensitive to doxorubicin

References:

Genotypes:

FYPO:0007931 - sensitive to egtazic acid

References:

Genotypes:

FYPO:0000842 - sensitive to ethanol during vegetative growth

References:

Genotypes:

FYPO:0007928 - sensitive to ethylenediaminetetraacetic acid

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Genotypes:

FYPO:0000785 - sensitive to formamide

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Genotypes:

FYPO:0000087 - sensitive to hydrogen peroxide

References:

Genotypes:

FYPO:0000088 - sensitive to hydroxyurea

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Genotypes:

FYPO:0000267 - sensitive to ionizing radiation during vegetative growth

References:

Genotypes:

FYPO:0001719 - sensitive to lithium

References:

Genotypes:

FYPO:0009086 - sensitive to lithium chloride and sodium dodecyl sulfate

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Genotypes:

FYPO:0009088 - sensitive to magnesium chloride and sodium dodecyl sulfate

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Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

References:

Genotypes:

FYPO:0002641 - sensitive to micafungin

References:

Genotypes:

FYPO:0001214 - sensitive to potassium chloride

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Genotypes:

FYPO:0007924 - sensitive to potassium chloride and sodium dodecyl sulfate

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Genotypes:

FYPO:0000271 - sensitive to salt stress

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Genotypes:

FYPO:0009090 - sensitive to sodium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0007938 - sensitive to tea tree oil

References:

Genotypes:

FYPO:0002701 - sensitive to torin1

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Genotypes:

FYPO:0002546 - sensitive to trichostatin A

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Genotypes:

FYPO:0001457 - sensitive to tunicamycin

References:

Genotypes:

FYPO:0000115 - sensitive to valproic acid

References:

Genotypes:

FYPO:0003656 - sensitive to vanadate

References:

Genotypes:

FYPO:0009064 - sensitive to X-rays and rapamycin during vegetative growth.

References:

Genotypes:

FYPO:0009063 - sensitive to X-rays during vegetative growth

References:

Genotypes:

FYPO:0000647 - vegetative cell lysis

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

FYPO:0002177 - viable vegetative cell with normal cell morphology

References:

Genotypes:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Warnings

PBO:0000070 - gene structure updated

References:

Protein features

IDNameInterPro nameDB name
PF04857CAF1RNase_CAF1Pfam
G3DSA:3.30.420.10:FF:000048CATH-FunFam
G3DSA:3.30.420.10RNaseH_sfCATH-Gene3D
SSF53098RNaseH-like_sfSUPERFAMILY
PTHR10797CNOT7/CNOT8/Pop2PANTHER
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Polardisorder_predictionMobiDB-Polar

Orthologs

References / Literature

PMID:24713849 - Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex.
Egan ED et al. RNA 2014 Jun;20(6):867-81
PMID:26804377 - The architecture of the Schizosaccharomyces pombe CCR4-NOT complex.
Ukleja M et al. Nat Commun 2016 Jan 25;7:10433
PMID:28404620 - Accumulation of RNA on chromatin disrupts heterochromatic silencing.
Brönner C et al. Genome Res 2017 Jul;27(7):1174-1183
PMID:23738021 - A genome-wide screening of potential target genes to enhance the antifungal activity of micafungin in Schizosaccharomyces pombe.
Zhou X et al. PLoS One 2013;8(5):e65904
PMID:25375137 - Systematic analysis of the role of RNA-binding proteins in the regulation of RNA stability.
Hasan A et al. PLoS Genet 2014 Nov;10(11):e1004684
PMID:27053105 - Mga2 Transcription Factor Regulates an Oxygen-responsive Lipid Homeostasis Pathway in Fission Yeast.
Burr R et al. J Biol Chem 2016 Jun 03;291(23):12171-83
PMID:37279920 - A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading.
Challal D et al. Genetics 2023 Aug 09;224(4)
PMID:27851962 - Reconstitution of Targeted Deadenylation by the Ccr4-Not Complex and the YTH Domain Protein Mmi1.
Stowell JAW et al. Cell Rep 2016 Nov 15;17(8):1978-1989
PMID:18684775 - A genome-wide screen of genes involved in cadmium tolerance in Schizosaccharomyces pombe.
Kennedy PJ et al. Toxicol Sci 2008 Nov;106(1):124-39
PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:39761853 - Regulation of sod1 mRNA and protein abundance by zinc in fission yeast is dependent on the CCR4-NOT complex.
Weeks AT et al. J Biol Chem 2025 Jan 04;:108156
PMID:23950735 - Global analysis of fission yeast mating genes reveals new autophagy factors.
Sun LL et al. PLoS Genet 2013;9(8):e1003715
PMID:29259000 - Genes Important for Schizosaccharomyces pombe Meiosis Identified Through a Functional Genomics Screen.
Blyth J et al. Genetics 2018 Feb;208(2):589-603
PMID:18257517 - Phosphoproteome analysis of fission yeast.
Wilson-Grady JT et al. J Proteome Res 2008 Mar;7(3):1088-97
PMID:23365689 - Cellular robustness conferred by genetic crosstalk underlies resistance against chemotherapeutic drug doxorubicin in fission yeast.
Tay Z et al. PLoS One 2013;8(1):e55041
PMID:20537132 - Global fitness profiling of fission yeast deletion strains by barcode sequencing.
Han TX et al. Genome Biol 2010;11(6):R60
PMID:28545058 - A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control.
Kume K et al. PLoS Genet 2017 May;13(5):e1006767
PMID:37445861 - Resistance to Chemotherapeutic 5-Fluorouracil Conferred by Modulation of Heterochromatic Integrity through Ino80 Function in Fission Yeast.
Lim KK et al. Int J Mol Sci 2023 Jun 26;24(13)
PMID:37787768 - Broad functional profiling of fission yeast proteins using phenomics and machine learning.
Rodríguez-López M et al. Elife 2023 Oct 03;12
PMID:22737087 - The CCR4-NOT complex is implicated in the viability of aneuploid yeasts.
Tange Y et al. PLoS Genet 2012;8(6):e1002776
PMID:18818364 - Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.
Roguev A et al. Science 2008 Oct 17;322(5900):405-10
PMID:19264558 - Screening a genome-wide S. pombe deletion library identifies novel genes and pathways involved in genome stability maintenance.
Deshpande GP et al. DNA Repair (Amst) 2009 May 01;8(5):672-9
PMID:28841135 - Ubiquitination-dependent control of sexual differentiation in fission yeast.
Simonetti F et al. Elife 2017 Aug 25;6
PMID:41184513 - Phosphorylation-dependent tuning of mRNA deadenylation rates.
Stowell JAW et al. Nat Struct Mol Biol 2025 Nov 03;
PMID:19672306 - Genome-wide screen of genes required for caffeine tolerance in fission yeast.
Calvo IA et al. PLoS One 2009 Aug 12;4(8):e6619
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:26942678 - Enhancer of Rudimentary Cooperates with Conserved RNA-Processing Factors to Promote Meiotic mRNA Decay and Facultative Heterochromatin Assembly.
Sugiyama T et al. Mol Cell 2016 Mar 03;61(5):747-759
PMID:24095277 - Argonaute and Triman generate dicer-independent priRNAs and mature siRNAs to initiate heterochromatin formation.
Marasovic M et al. Mol Cell 2013 Oct 24;52(2):173-83
PMID:29996109 - Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe.
Swaffer MP et al. Cell Rep 2018 Jul 10;24(2):503-514
PMID:24013502 - Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries.
Wang J et al. Genes Dev 2013 Sep 01;27(17):1886-902
PMID:30601114 - RNA-binding proteins distinguish between similar sequence motifs to promote targeted deadenylation by Ccr4-Not.
Webster MW et al. Elife 2019 Jan 02;8
PMID:29932902 - mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases.
Webster MW et al. Mol Cell 2018 Jun 21;70(6):1089-1100.e8
PMID:33260998 - High-Throughput Flow Cytometry Combined with Genetic Analysis Brings New Insights into the Understanding of Chromatin Regulation of Cellular Quiescence.
Zahedi Y et al. Int J Mol Sci 2020 Nov 27;21(23)
PMID:40015273 - A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.
Skribbe M et al. Mol Cell 2025 Feb 19;
PMID:26771498 - A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.
Vo TV et al. Cell 2016 Jan 14;164(1-2):310-323
PMID:41844616 - Phosphoregulation of the novel hemi-arrestin MAPK scaffold Sms1 prevents untimely mating.
Sieber B et al. Nat Commun 2026 Mar 17;
PMID:26891792 - Calcium modulation of doxorubicin cytotoxicity in yeast and human cells.
Nguyen TT et al. Genes Cells 2016 Mar;21(3):226-40
PMID:17452359 - The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme.
Jonstrup AT et al. Nucleic Acids Res 2007;35(9):3153-64
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.
Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:31883795 - Positioning Heterochromatin at the Nuclear Periphery Suppresses Histone Turnover to Promote Epigenetic Inheritance.
Holla S et al. Cell 2020 Jan 09;180(1):150-164.e15
PMID:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.
Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
PMID:19307292 - The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site.
Andersen KR et al. RNA 2009 May;15(5):850-61
PMID:17264117 - Caf1 regulates translocation of ribonucleotide reductase by releasing nucleoplasmic Spd1-Suc22 assembly.
Takahashi S et al. Nucleic Acids Res 2007;35(4):1187-97
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Halova L et al. Open Biol 2021 Apr;11(4):200405