protein coding gene - clr4 (SPBC428.08c) - histone lysine H3-K9 methyltransferase (Suv39) Clr4

Gene summary

Standard name

clr4

Systematic ID

SPBC428.08c

Product

histone lysine H3-K9 methyltransferase (Suv39) Clr4

Organism

Schizosaccharomyces pombe (fission yeast)

UniProt ID

O60016

ORFeome ID

23/23G02

Characterisation status

biological role published

Feature type

mRNA gene

Genomic location

chromosome II: 453996..458410 reverse strand

Annotation

Protein features

Orthologs

• SUV39H1 (HGNC:11479) Homo sapiens
• SUV39H2 (HGNC:17287) Homo sapiens
• clr4 (SJAG_04574) Schizosaccharomyces japonicus

References / Literature

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Marguerat S et al. Cell 2012 Oct 26;151(3):671-83

PMID:21253571 - H3K9me-independent gene silencing in fission yeast heterochromatin by Clr5 and histone deacetylases.

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PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.

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PMID:40132111 - A fission yeast CENP-B homologue Abp1 prevents RNAi-mediated heterochromatin formation at ribosomal DNA repeats.

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PMID:22990236 - Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin.

Shim YS et al. EMBO J 2012 Nov 28;31(23):4375-87

PMID:23173672 - Identification of novel genes involved in DNA damage response by screening a genome-wide Schizosaccharomyces pombe deletion library.

Pan X et al. BMC Genomics 2012 Nov 23;13:662

PMID:29216371 - Fission yeast Ccq1 is a modulator of telomerase activity.

Armstrong CA et al. Nucleic Acids Res 2018 Jan 25;46(2):704-716

PMID:20062003 - Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast.

Simmer F et al. EMBO Rep 2010 Feb;11(2):112-8

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:18957202 - Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin.

Li F et al. Cell 2008 Oct 17;135(2):272-83

PMID:29136238 - Regulation of transcriptional silencing and chromodomain protein localization at centromeric heterochromatin by histone H3 tyrosine 41 phosphorylation in fission yeast.

Ren B et al. Nucleic Acids Res 2018 Jan 09;46(1):189-202

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:28143796 - Clr4 specificity and catalytic activity beyond H3K9 methylation.

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PMID:29852001 - New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe.

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PMID:18505873 - Schizosaccharomyces pombe histone acetyltransferase Mst1 (KAT5) is an essential protein required for damage response and chromosome segregation.

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PMID:25619765 - The CENP-A N-tail confers epigenetic stability to centromeres via the CENP-T branch of the CCAN in fission yeast.

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PMID:15218150 - RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins.

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PMID:17512405 - RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing.

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PMID:18761674 - Fission yeast chromatin assembly factor 1 assists in the replication-coupled maintenance of heterochromatin.

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PMID:23851719 - Spt6 prevents transcription-coupled loss of posttranslationally modified histone H3.

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PMID:36830746 - Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast.

Takahata S et al. Biomolecules 2023 Feb 16;13(2)

PMID:25452419 - Parallel profiling of fission yeast deletion mutants for proliferation and for lifespan during long-term quiescence.

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PMID:30051891 - Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability.

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PMID:28318821 - SNF2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance and Proper Replication.

Taneja N et al. Mol Cell 2017 Apr 06;66(1):50-62.e6

PMID:40923761 - Intrinsically disordered region of Clr4/Suv39 regulates its enzymatic activity and ensures heterochromatin spreading.

Nakamura R et al. Nucleic Acids Res 2025 Sep 05;53(17)

PMID:27264871 - Taz1-Shelterin Promotes Facultative Heterochromatin Assembly at Chromosome-Internal Sites Containing Late Replication Origins.

Zofall M et al. Mol Cell 2016 Jun 16;62(6):862-874

PMID:15292231 - Regulation of Swi6/HP1-dependent heterochromatin assembly by cooperation of components of the mitogen-activated protein kinase pathway and a histone deacetylase Clr6.

Kim HS et al. J Biol Chem 2004 Oct 08;279(41):42850-9

PMID:21385875 - Roles of fission yeast Grc3 protein in ribosomal RNA processing and heterochromatic gene silencing.

Kitano E et al. J Biol Chem 2011 Apr 29;286(17):15391-402

PMID:27334362 - Inner nuclear membrane protein Lem2 augments heterochromatin formation in response to nutritional conditions.

Tange Y et al. Genes Cells 2016 Aug;21(8):812-32

PMID:31278118 - Cohesin Impedes Heterochromatin Assembly in Fission Yeast Cells Lacking Pds5.

Folco HD et al. Genetics 2019 Sep;213(1):127-141

PMID:19111658 - HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms.

Motamedi MR et al. Mol Cell 2008 Dec 26;32(6):778-90

PMID:32499408 - The molecular chaperone Hsp90 regulates heterochromatin assembly through stabilizing multiple complexes in fission yeast.

Sun L et al. J Cell Sci 2020 Jul 07;133(13)

PMID:8001791 - Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe.

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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

PMID:10949293 - Regulation of chromatin structure by site-specific histone H3 methyltransferases.

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PMID:12161753 - The transcriptional program of meiosis and sporulation in fission yeast.

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PMID:11069763 - Live analysis of lagging chromosomes during anaphase and their effect on spindle elongation rate in fission yeast.

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PMID:16428807 - Hip3 interacts with the HIRA proteins Hip1 and Slm9 and is required for transcriptional silencing and accurate chromosome segregation.

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PMID:34375584 - A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin.

Wang X et al. Mol Cell 2021 Oct 07;81(19):3979-3991.e4

PMID:15372076 - A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast.

Sadaie M et al. EMBO J 2004 Oct 01;23(19):3825-35

PMID:23388053 - Transcription-induced chromatin association of RNA surveillance factors mediates facultative heterochromatin formation in fission yeast.

Tashiro S et al. Genes Cells 2013 Apr;18(4):327-39

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:19362535 - High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin.

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PMID:15537537 - Heterochromatin regulates cell type-specific long-range chromatin interactions essential for directed recombination.

Jia S et al. Cell 2004 Nov 12;119(4):469-80

PMID:12867036 - Sir2 regulates histone H3 lysine 9 methylation and heterochromatin assembly in fission yeast.

Shankaranarayana GD et al. Curr Biol 2003 Jul 15;13(14):1240-6

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:27697832 - Rad51 and Rad54 promote noncrossover recombination between centromere repeats on the same chromatid to prevent isochromosome formation.

Onaka AT et al. Nucleic Acids Res 2016 Dec 15;44(22):10744-10757

GO_REF:0000002 - Comments

PMID:21151114 - Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe.

Woolcock KJ et al. Nat Struct Mol Biol 2011 Jan;18(1):94-9

PMID:29722648 - Distinct 'safe zones' at the nuclear envelope ensure robust replication of heterochromatic chromosome regions.

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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: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:19693008 - Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs.

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PMID:9572142 - Defective meiosis in telomere-silencing mutants of Schizosaccharomyces pombe.

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PMID:18818364 - Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

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PMID:17948055 - The JmjC domain protein Epe1 prevents unregulated assembly and disassembly of heterochromatin.

Trewick SC et al. EMBO J 2007 Nov 14;26(22):4670-82

PMID:27648579 - A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading.

Shan CM et al. Elife 2016 Sep 20;5

PMID:28682306 - Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription.

Jih G et al. Nature 2017 Jul 27;547(7664):463-467

PMID:27984744 - Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.

Joh RI et al. Mol Cell 2016 Dec 15;64(6):1088-1101

PMID:29686279 - Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control.

Gallagher PS et al. Nat Struct Mol Biol 2018 May;25(5):372-383

PMID:29784772 - A Heterochromatin Domain Forms Gradually at a New Telomere and Is Dynamic at Stable Telomeres.

Wang J et al. Mol Cell Biol 2018 Aug 01;38(15)

PMID:27738016 - RNA interference is essential for cellular quiescence.

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PMID:23260662 - Lsd1 and lsd2 control programmed replication fork pauses and imprinting in fission yeast.

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PMID:11283354 - Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly.

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PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.

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PMID:23936074 - Telomeric repeats facilitate CENP-A(Cnp1) incorporation via telomere binding proteins.

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PMID:23050226 - A genetic screen to discover pathways affecting cohesin function in Schizosaccharomyces pombe identifies chromatin effectors.

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PMID:29167439 - Eroded telomeres are rearranged in quiescent fission yeast cells through duplications of subtelomeric sequences.

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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:8937982 - Mutations in the fission yeast silencing factors clr4+ and rik1+ disrupt the localisation of the chromo domain protein Swi6p and impair centromere function.

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PMID:12389037 - Structure of the SET domain histone lysine methyltransferase Clr4.

Min J et al. Nat Struct Biol 2002 Nov;9(11):828-32

PMID:16127433 - Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin.

Jia S et al. Nat Cell Biol 2005 Oct;7(10):1007-13

PMID:27298342 - Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks.

Willis NA et al. Proc Natl Acad Sci U S A 2016 Jun 28;113(26):E3676-85

PMID:30652128 - Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription.

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PMID:28765164 - Selective termination of lncRNA transcription promotes heterochromatin silencing and cell differentiation.

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PMID:30089114 - Heterochromatin and RNAi regulate centromeres by protecting CENP-A from ubiquitin-mediated degradation.

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PMID:18923422 - Rad51 suppresses gross chromosomal rearrangement at centromere in Schizosaccharomyces pombe.

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PMID:33378674 - The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin.

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PMID:41316862 - Deletion of Elongator Protein 1 (Elp1) relieves heterochromatin defects in a Pol II mutant of Schizosaccharomyces pombe.

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PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.

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PMID:38181050 - The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe.

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PMID:8138176 - Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast.

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PMID:19264558 - Screening a genome-wide S. pombe deletion library identifies novel genes and pathways involved in genome stability maintenance.

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PMID:26988418 - The proper connection between shelterin components is required for telomeric heterochromatin assembly.

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PMID:29237752 - Ser7 of RNAPII-CTD facilitates heterochromatin formation by linking ncRNA to RNAi.

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PMID:39786922 - The fission yeast SUMO-targeted ubiquitin ligase Slx8 functionally associates with clustered centromeres and the silent mating-type region at the nuclear periphery.

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PMID:34731638 - The histone chaperone FACT facilitates heterochromatin spreading by regulating histone turnover and H3K9 methylation states.

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PMID:23849629 - Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread.

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PMID:25957277 - Intrinsic Toxicity of Unchecked Heterochromatin Spread Is Suppressed by Redundant Chromatin Boundary Functions in Schizosacchromyces pombe.

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PMID:39094565 - Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation.

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PMID:15947136 - RNA polymerase II is required for RNAi-dependent heterochromatin assembly.

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PMID:16168376 - SUMO modification is involved in the maintenance of heterochromatin stability in fission yeast.

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PMID:22683269 - HP1(Swi6) mediates the recognition and destruction of heterochromatic RNA transcripts.

Keller C et al. Mol Cell 2012 Jul 27;47(2):215-27

PMID:37787768 - Broad functional profiling of fission yeast proteins using phenomics and machine learning.

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PMID:26744419 - Control of heterochromatin localization and silencing by the nuclear membrane protein Lem2.

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PMID:15197176 - The fission yeast heterochromatin protein Rik1 is required for telomere clustering during meiosis.

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PMID:37400983 - Cooperative DNA-binding activities of Chp2 are critical for its function in heterochromatin assembly.

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PMID:38289024 - Heat stress-induced activation of MAPK pathway attenuates Atf1-dependent epigenetic inheritance of heterochromatin in fission yeast.

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PMID:24095277 - Argonaute and Triman generate dicer-independent priRNAs and mature siRNAs to initiate heterochromatin formation.

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PMID:12750522 - Distinct cohesin complexes organize meiotic chromosome domains.

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PMID:26582768 - Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organisation.

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PMID:10835380 - Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations.

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PMID:22895252 - A novel RNAi protein, Dsh1, assembles RNAi machinery on chromatin to amplify heterochromatic siRNA.

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PMID:31206516 - Regulation of ectopic heterochromatin-mediated epigenetic diversification by the JmjC family protein Epe1.

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PMID:24240238 - Elimination of shelterin components bypasses RNAi for pericentric heterochromatin assembly.

Tadeo X et al. Genes Dev 2013 Nov 15;27(22):2489-99

PMID:25774602 - Rapid epigenetic adaptation to uncontrolled heterochromatin spreading.

Wang J et al. Elife 2015 Mar 16;4

PMID:26804021 - Shugoshin forms a specialized chromatin domain at subtelomeres that regulates transcription and replication timing.

Tashiro S et al. Nat Commun 2016 Jan 25;7:10393

PMID:18216783 - Cell cycle control of centromeric repeat transcription and heterochromatin assembly.

Chen ES et al. Nature 2008 Feb 07;451(7179):734-7

PMID:34984977 - Functional profiling of long intergenic non-coding RNAs in fission yeast.

Rodriguez-Lopez M et al. Elife 2022 Jan 05;11

PMID:22474355 - Heterochromatin protein 1 homologue Swi6 acts in concert with Ers1 to regulate RNAi-directed heterochromatin assembly.

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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:36200823 - The chromatin remodeler RSC prevents ectopic CENP-A propagation into pericentromeric heterochromatin at the chromatin boundary.

Tsunemine S et al. Nucleic Acids Res 2022 Oct 28;50(19):10914-10928

PMID:18948543 - Splicing factors facilitate RNAi-directed silencing in fission yeast.

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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:29618061 - Histone deacetylation promotes transcriptional silencing at facultative heterochromatin.

Watts BR et al. Nucleic Acids Res 2018 Jun 20;46(11):5426-5440

PMID:23028377 - Factors that promote H3 chromatin integrity during transcription prevent promiscuous deposition of CENP-A(Cnp1) in fission yeast.

Choi ES et al. PLoS Genet 2012 Sep;8(9):e1002985

PMID:21436456 - Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA.

Zhang K et al. Science 2011 Mar 25;331(6024):1624-7

PMID:20705239 - The methyltransferase activity of Clr4Suv39h triggers RNAi independently of histone H3K9 methylation.

Gerace EL et al. Mol Cell 2010 Aug 13;39(3):360-72

PMID:33511417 - Repression of a large number of genes requires interplay between homologous recombination and HIRA.

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PMID:15475954 - RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing.

Noma K et al. Nat Genet 2004 Nov;36(11):1174-80

PMID:15615848 - RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production.

Sugiyama T et al. Proc Natl Acad Sci U S A 2005 Jan 04;102(1):152-7

PMID:18716626 - Heterochromatin links to centromeric protection by recruiting shugoshin.

Yamagishi Y et al. Nature 2008 Sep 11;455(7210):251-5

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:25002536 - A novel histone deacetylase complex in the control of transcription and genome stability.

Zilio N et al. Mol Cell Biol 2014 Sep 15;34(18):3500-14

PMID:24493644 - lncRNA recruits RNAi and the exosome to dynamically regulate pho1 expression in response to phosphate levels in fission yeast.

Shah S et al. Genes Dev 2014 Feb 01;28(3):231-44

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:18252195 - Methylations of histone H3 lysine 9 and lysine 36 are functionally linked to DNA replication checkpoint control in fission yeast.

Kim HS et al. Biochem Biophys Res Commun 2008 Apr 04;368(2):419-25

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:29084823 - Phosphorylation of the RNA-binding protein Zfs1 modulates sexual differentiation in fission yeast.

Navarro FJ et al. J Cell Sci 2017 Dec 15;130(24):4144-4154

PMID:20537132 - Global fitness profiling of fission yeast deletion strains by barcode sequencing.

Han TX et al. Genome Biol 2010;11(6):R60

PMID:29294138 - Editor's Highlight: A Genome-wide Screening of Target Genes Against Silver Nanoparticles in Fission Yeast.

Lee AR et al. Toxicol Sci 2018 Jan 01;161(1):171-185

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:16762840 - Swi6/HP1 recruits a JmjC domain protein to facilitate transcription of heterochromatic repeats.

Zofall M et al. Mol Cell 2006 Jun 09;22(5):681-92

PMID:20178743 - Dicer-independent primal RNAs trigger RNAi and heterochromatin formation.

Halic M et al. Cell 2010 Feb 19;140(4):504-16

PMID:41525994 - Transcriptional PBR cycles at pericentromeric repeats cause gross chromosomal rearrangements through Rad52-dependent ADR-loop formation.

Xu R et al. Nucleic Acids Res 2026 Jan 05;54(1)

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:22727667 - Intrinsic nucleic acid-binding activity of Chp1 chromodomain is required for heterochromatic gene silencing.

Ishida M et al. Mol Cell 2012 Jul 27;47(2):228-41

PMID:36408846 - Differential phosphorylation of Clr4 SUV39H by Cdk1 accompanies a histone H3 methylation switch that is essential for gametogenesis.

Kuzdere T et al. EMBO Rep 2023 Jan 09;24(1):e55928

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:22319459 - Raf1 Is a DCAF for the Rik1 DDB1-like protein and has separable roles in siRNA generation and chromatin modification.

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