PomBase home

protein coding gene - raf2 (SPCC970.07c) - CLRC ubiquitin ligase complex subunit Raf2

Gene summary

Standard name
raf2
Systematic ID
SPCC970.07c
Product
CLRC ubiquitin ligase complex subunit Raf2
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
dos2, cmc2, clr7
UniProt ID
O74560
ORFeome ID
26/26F09
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome III: 500765..502880 forward strand

Annotation

Disease association

MONDO:0011397 - autosomal dominant cerebellar ataxia, deafness and narcolepsy

References:

MONDO:0013584 - hereditary sensory neuropathy-deafness-dementia syndrome

References:

GO biological process

GO:0034080 - CENP-A containing chromatin assembly

References:

GO:0030466 - silent mating-type cassette heterochromatin formation

References:

GO:0140727 - siRNA-mediated pericentric heterochromatin formation

References:

GO:0031509 - subtelomeric heterochromatin formation

References:

GO cellular component

GO:0043494 - CLRC complex

References:

GO:0005737 - cytoplasm

References:

GO:1990342 - heterochromatin island

References:

GO:0031934 - mating-type region heterochromatin

References:

GO:0005634 - nucleus

References:

GO:0005721 - pericentric heterochromatin

References:

GO:0033553 - rDNA heterochromatin

References:

GO:0140720 - subtelomeric heterochromatin

References:

GO molecular function

GO:0005515 - protein binding

References:

Modification

MOD:00047 - O-phospho-L-threonine

References:

MOD:00048 - O4'-phospho-L-tyrosine

References:

Multi-locus phenotype

FYPO:0007597 - abolished CLRC complex binding

References:

Genotypes:

FYPO:0005850 - abolished protein localization to heterochromatin at centromere outer repeat

References:

Genotypes:

FYPO:0000082 - decreased cell population growth at high temperature

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0007629 - normal viability during G0

References:

Genotypes:

Protein features

PBO:0111947 - zf-basic zinc finger

References:

PBO:0111743 - zinc finger protein

References:

Quantitative gene expression

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0000468 - abnormal mating type switching

References:

Genotypes:

FYPO:0000151 - abnormal meiotic chromosome segregation

References:

Genotypes:

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

References:

Genotypes:

FYPO:0005850 - abolished protein localization to heterochromatin at centromere outer repeat

References:

Genotypes:

FYPO:0001978 - bent mitotic spindle

References:

Genotypes:

FYPO:0000250 - decreased cell population growth on proline nitrogen source

References:

Genotypes:

FYPO:0002834 - decreased chromatin silencing at centromere

References:

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:0004904 - decreased protein localization to centromere central core during vegetative growth

References:

Genotypes:

FYPO:0002019 - elongated telomeres during vegetative growth

References:

Genotypes:

FYPO:0009094 - increased cell population growth on lysine and proline nitrogen source

References:

Genotypes:

FYPO:0009072 - increased cell population growth on lysine nitrogen source

References:

Genotypes:

FYPO:0002836 - increased centromeric outer repeat transcript-derived siRNA level

References:

Genotypes:

FYPO:0005063 - increased histone H3-K4 methylation at mating type locus during vegetative growth

References:

Genotypes:

FYPO:0001840 - increased minichromosome loss during vegetative growth

References:

Genotypes:

FYPO:0001327 - increased protein level during vegetative growth

References:

Genotypes:

FYPO:0001309 - increased viability in stationary phase

References:

Genotypes:

FYPO:0004909 - loss of punctate nuclear protein localization, with protein distributed in nucleus

References:

Genotypes:

FYPO:0006518 - loss of viability in G0

References:

Genotypes:

FYPO:0000674 - normal cell population growth at high temperature

References:

Genotypes:

FYPO:0002141 - normal cell population growth at low temperature

References:

Genotypes:

FYPO:0002837 - normal centromeric outer repeat transcript-derived siRNA level

References:

Genotypes:

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

References:

Genotypes:

FYPO:0007553 - normal G1 to G0 transition

References:

Genotypes:

FYPO:0001164 - normal growth on glucose carbon source

References:

Genotypes:

FYPO:0000833 - normal protein level during vegetative growth

References:

Genotypes:

FYPO:0002574 - normal protein localization to centromere during vegetative growth

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0007629 - normal viability during G0

References:

Genotypes:

FYPO:0009030 - resistance to amitrole

References:

Genotypes:

FYPO:0002693 - resistance to diamide

References:

Genotypes:

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

References:

Genotypes:

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

References:

Genotypes:

FYPO:0004325 - sensitive to 5-fluorouracil

References:

Genotypes:

FYPO:0000084 - sensitive to 6-azauracil

References:

Genotypes:

FYPO:0002642 - sensitive to amphotericin B

References:

Genotypes:

FYPO:0001701 - sensitive to bortezomib

References:

Genotypes:

FYPO:0006930 - sensitive to butylated hydroxyanisole

References:

Genotypes:

FYPO:0000096 - sensitive to cadmium

References:

Genotypes:

FYPO:0007931 - sensitive to egtazic acid

References:

Genotypes:

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

References:

Genotypes:

FYPO:0002641 - sensitive to micafungin

References:

Genotypes:

FYPO:0003241 - unequal mitotic sister chromatid segregation

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:0000055 - no apparent S. cerevisiae ortholog

Protein features

IDNameInterPro nameDB name
PF12047DNMT1-RFDDNMT1-RFDPFAM

Orthologs

References / Literature

PMID:38181050 - The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe.
Liu H et al. PLoS Genet 2024 Jan 05;20(1):e1011107
PMID:20625380 - A genome-wide screen for Schizosaccharomyces pombe deletion mutants that affect telomere length.
Liu NN et al. Cell Res 2010 Aug;20(8):963-5
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: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: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:26631744 - Conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing.
Chalamcharla VR et al. Proc Natl Acad Sci U S A 2015 Dec 22;112(51):15548-55
PMID:27738016 - RNA interference is essential for cellular quiescence.
Roche B et al. Science 2016 Nov 11;354(6313)
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:22681890 - Hierarchical modularity and the evolution of genetic interactomes across species.
Ryan CJ et al. Mol Cell 2012 Jun 08;46(5):691-704
PMID:18345014 - Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin.
Zhang K et al. Nat Struct Mol Biol 2008 Apr;15(4):381-8
PMID:16024659 - A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation.
Horn PJ et al. Genes Dev 2005 Jul 15;19(14):1705-14
PMID:22319459 - Raf1 Is a DCAF for the Rik1 DDB1-like protein and has separable roles in siRNA generation and chromatin modification.
Buscaino A et al. PLoS Genet 2012 Feb;8(2):e1002499
PMID:22474355 - Heterochromatin protein 1 homologue Swi6 acts in concert with Ers1 to regulate RNAi-directed heterochromatin assembly.
Hayashi A et al. Proc Natl Acad Sci U S A 2012 Apr 17;109(16):6159-64
PMID:26670050 - Regulation of mRNA Levels by Decay-Promoting Introns that Recruit the Exosome Specificity Factor Mmi1.
Kilchert C et al. Cell Rep 2015 Dec 22;13(11):2504-2515
PMID:31278118 - Cohesin Impedes Heterochromatin Assembly in Fission Yeast Cells Lacking Pds5.
Folco HD et al. Genetics 2019 Sep;213(1):127-141
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:21725325 - Coordination of DNA replication and histone modification by the Rik1-Dos2 complex.
Li F et al. Nature 2011 Jul 03;475(7355):244-8
PMID:23050226 - A genetic screen to discover pathways affecting cohesin function in Schizosaccharomyces pombe identifies chromatin effectors.
Chen Z et al. G3 (Bethesda) 2012 Oct;2(10):1161-8
PMID:26173815 - Genome-wide screen of fission yeast mutants for sensitivity to 6-azauracil, an inhibitor of transcriptional elongation.
Zhou H et al. Yeast 2015 Oct;32(10):643-55
PMID:39747188 - PhpC NF-Y transcription factor infiltrates heterochromatin to generate cryptic intron-containing transcripts crucial for small RNA production.
Srivastav MK et al. Nat Commun 2025 Jan 02;16(1):268
PMID:20211136 - Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity.
Bayne EH et al. Cell 2010 Mar 05;140(5):666-77
PMID:23613586 - Structural analysis of Stc1 provides insights into the coupling of RNAi and chromatin modification.
He C et al. Proc Natl Acad Sci U S A 2013 May 21;110(21):E1879-88
PMID:26988418 - The proper connection between shelterin components is required for telomeric heterochromatin assembly.
Wang J et al. Genes Dev 2016 Apr 01;30(7):827-39
PMID:27538348 - Set3 contributes to heterochromatin integrity by promoting transcription of subunits of Clr4-Rik1-Cul4 histone methyltransferase complex in fission yeast.
Yu Y et al. Sci Rep 2016 Aug 19;6:31752
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: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:16040243 - Two novel proteins, dos1 and dos2, interact with rik1 to regulate heterochromatic RNA interference and histone modification.
Li F et al. Curr Biol 2005 Aug 23;15(16):1448-57
PMID:25076038 - Large scale screening of genetic interaction with sgf73(+) in fission yeast.
Guo Y et al. Yi Chuan 2014 Jul;36(7):723-31
PMID:22144463 - RNA elimination machinery targeting meiotic mRNAs promotes facultative heterochromatin formation.
Zofall M et al. Science 2012 Jan 06;335(6064):96-100
PMID:28228545 - Ablation of RNA interference and retrotransposons accompany acquisition and evolution of transposases to heterochromatin protein CENPB.
Upadhyay U et al. Mol Biol Cell 2017 Apr 15;28(8):1132-1146
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
PMID:16157682 - The Clr7 and Clr8 directionality factors and the Pcu4 cullin mediate heterochromatin formation in the fission yeast Schizosaccharomyces pombe.
Thon G et al. Genetics 2005 Dec;171(4):1583-95
PMID:17114925 - A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation.
Hong EJ et al. RNA Biol 2005;2(3):106-11
PMID:21060862 - Continuous requirement for the Clr4 complex but not RNAi for centromeric heterochromatin assembly in fission yeast harboring a disrupted RITS complex.
Shanker S et al. PLoS Genet 2010 Oct 28;6(10):e1001174
PMID:25274039 - A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast.
Bayne EH et al. Genome Biol 2014;15(10):481
PMID:25090107 - The RFTS domain of Raf2 is required for Cul4 interaction and heterochromatin integrity in fission yeast.
White SA et al. PLoS One 2014;9(8):e104161
PMID:25972440 - Global regulation of heterochromatin spreading by Leo1.
Verrier L et al. Open Biol 2015 May;5(5)
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: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:21760946 - Identification of genes affecting the toxicity of anti-cancer drug bortezomib by genome-wide screening in S. pombe.
Takeda K et al. PLoS One 2011;6(7):e22021
PMID:34010645 - The histone H3K9M mutation synergizes with H3K14 ubiquitylation to selectively sequester histone H3K9 methyltransferase Clr4 at heterochromatin.
Shan CM et al. Cell Rep 2021 May 18;35(7):109137
PMID:35820914 - Antagonistic effects of mitochondrial matrix and intermembrane space proteases on yeast aging.
Vega M et al. BMC Biol 2022 Jul 12;20(1):160
PMID:23267073 - Cell cycle-dependent deposition of CENP-A requires the Dos1/2-Cdc20 complex.
Gonzalez M et al. Proc Natl Acad Sci U S A 2013 Jan 08;110(2):606-11
PMID:25245948 - Tls1 regulates splicing of shelterin components to control telomeric heterochromatin assembly and telomere length.
Wang J et al. Nucleic Acids Res 2014 Oct;42(18):11419-32
PMID:21504829 - Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex.
Stewart EV et al. Mol Cell 2011 Apr 22;42(2):160-71
PMID:30647105 - Comparative Genomic Screen in Two Yeasts Reveals Conserved Pathways in the Response Network to Phenol Stress.
Alhoch B et al. G3 (Bethesda) 2019 Mar 07;9(3):639-650
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:24449894 - CRL4-like Clr4 complex in Schizosaccharomyces pombe depends on an exposed surface of Dos1 for heterochromatin silencing.
Kuscu C et al. Proc Natl Acad Sci U S A 2014 Feb 04;111(5):1795-800
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