SCHPO:CLR4

Species (Taxon ID)	Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast). (284812)
Gene Name(s)	clr4 (synonyms: kmt1)
Protein Name(s)	Histone-lysine N-methyltransferase, H3 lysine-9 specific Cryptic loci regulator 4 Histone H3-K9 methyltransferase H3-K9-HMTase Lysine N-methyltransferase 1
External Links
UniProt	O60016
EMBL	AF061854 AJ007840 CU329671
PIR	T43700 T43745
RefSeq	NP_595186.1
PDB	1G6Z 1MVH 1MVX 6BOX 6BP4
PDBsum	1G6Z 1MVH 1MVX 6BOX 6BP4
ProteinModelPortal	O60016
SMR	O60016
BioGrid	277343
DIP	DIP-32588N
IntAct	O60016
MINT	O60016
STRING	4896.SPBC428.08c.1
iPTMnet	O60016
MaxQB	O60016
PaxDb	O60016
PRIDE	O60016
EnsemblFungi	SPBC428.08c.1
GeneID	2540825
KEGG	spo:SPBC428.08c
EuPathDB	FungiDB:SPBC428.08c
PomBase	SPBC428.08c
InParanoid	O60016
KO	K11419
OMA	NCRGWLF
PhylomeDB	O60016
Reactome	R-SPO-3214841 R-SPO-427359
EvolutionaryTrace	O60016
PRO	PR:O60016
Proteomes	UP000002485
GO	GO:0034507 GO:0000781 GO:0043494 GO:0005737 GO:0031934 GO:0031618 GO:1990707 GO:0005634 GO:0005816 GO:0003690 GO:0046974 GO:0035064 GO:0008168 GO:0003697 GO:0003727 GO:0008270 GO:0034613 GO:0006338 GO:0030702 GO:0000183 GO:0030466 GO:0006348 GO:0007535 GO:1902368 GO:0045141 GO:0000122
CDD	cd00024
InterPro	IPR016197 IPR000953 IPR023780 IPR023779 IPR011381 IPR003616 IPR007728 IPR001214
Pfam	PF00385 PF05033 PF00856
PIRSF	PIRSF009343
SMART	SM00298 SM00508 SM00468 SM00317
SUPFAM	SSF54160
PROSITE	PS00598 PS50013 PS50868 PS50867 PS50280

Annotations

Qualifier	GO ID	GO term name	Reference	ECO ID	ECO term name	with/from	Aspect	Extension	Notes	Status
	GO:0090053	positive regulation of chromatin silencing at centromere	PMID:19136623^[1]	ECO:0000315			P		silencing defects in ckb1Δ cells was comparable with that caused by disruption of other heterochromatic genes, including clr4,Fig. 1B).	complete CACAO 11286
	GO:0030702	chromatin silencing at centromere	PMID:26889830^[2]	ECO:0000315			P		Figure 1B,C Similar to clr4Δ, dhp1-1 but not din1-null (din1Δ) cells form white colonies, indicating a silencing defect at the mating type locus unique to the dhp1 mutant.	complete CACAO 11327
	GO:0070829	heterochromatin maintenance	PMID:26889830^[2]	ECO:0000315			P		Figure 2A	complete CACAO 11329
	GO:1900111	positive regulation of histone H3-K9 dimethylation	PMID:26889830^[2]	ECO:0000315			P		Figure 2B&C show that levels of H3K9me2 at the reporter genes embedded in these regions were substantially reduced at these loci in cells deficient in dhp1	complete CACAO 11331
enables	GO:0046974	histone methyltransferase activity (H3-K9 specific)	PMID:10949293^[3]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0008168	methyltransferase activity	PMID:10949293^[3]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
part_of	GO:1990707	nuclear subtelomeric heterochromatin	GO_REF:0000051	ECO:0000303	author statement without traceable support used in manual assertion		C		Seeded From UniProt	complete
involved_in	GO:1990141	chromatin silencing at centromere outer repeat region	PMID:11283354^[4]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:1903212	protein localization to mating-type region heterochromatin	PMID:11283354^[4]	ECO:0000315	mutant phenotype evidence used in manual assertion		P	has_input:(PomBase:SPAC664.01c)	Seeded From UniProt	complete
involved_in	GO:1902682	protein localization to nuclear pericentric heterochromatin	PMID:11283354^[4]	ECO:0000315	mutant phenotype evidence used in manual assertion		P	has_input:(PomBase:SPAC664.01c)	Seeded From UniProt	complete
involved_in	GO:1902368	heterochromatin maintenance involved in chromatin silencing at centromere outer repeat region	PMID:23771057^[5]	ECO:0000316	genetic interaction evidence used in manual assertion	PomBase:SPBC16D10.07c	P		Seeded From UniProt	complete
enables	GO:0046974	histone methyltransferase activity (H3-K9 specific)	PMID:11283354^[4]	ECO:0000315	mutant phenotype evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0046974	histone methyltransferase activity (H3-K9 specific)	PMID:11283354^[4]	ECO:0000314	direct assay evidence used in manual assertion		F	occurs_at:(SO:0001799) part_of:(GO:1990141)	Seeded From UniProt	complete
enables	GO:0046974	histone methyltransferase activity (H3-K9 specific)	PMID:11283354^[4]	ECO:0000314	direct assay evidence used in manual assertion		F	occurs_at:(SO:0001798)	Seeded From UniProt	complete
enables	GO:0046974	histone methyltransferase activity (H3-K9 specific)	PMID:11283354^[4]	ECO:0000314	direct assay evidence used in manual assertion		F	occurs_at:(GO:0031934) part_of:(GO:0030466)	Seeded From UniProt	complete
enables	GO:0046974	histone methyltransferase activity (H3-K9 specific)	PMID:10949293^[3]	ECO:0000314	direct assay evidence used in manual assertion		F	has_direct_input:(PomBase:SPBC8D2.04)	Seeded From UniProt	complete
enables	GO:0046974	histone methyltransferase activity (H3-K9 specific)	PMID:10949293^[3]	ECO:0000314	direct assay evidence used in manual assertion		F	has_direct_input:(PomBase:SPBC1105.11c)	Seeded From UniProt	complete
enables	GO:0046974	histone methyltransferase activity (H3-K9 specific)	PMID:10949293^[3]	ECO:0000314	direct assay evidence used in manual assertion		F	has_direct_input:(PomBase:SPAC1834.04)	Seeded From UniProt	complete
involved_in	GO:0045141	meiotic telomere clustering	PMID:15197176^[6]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
part_of	GO:0043494	CLRC ubiquitin ligase complex	PMID:16127433^[7]	ECO:0000314	direct assay evidence used in manual assertion		C		Seeded From UniProt	complete
enables	GO:0035064	methylated histone binding	PMID:22727667^[8]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
involved_in	GO:0034613	cellular protein localization	PMID:15372076^[9]	ECO:0000315	mutant phenotype evidence used in manual assertion		P	has_input:(PomBase:SPBC16C6.10)	Seeded From UniProt	complete
involved_in	GO:0034613	cellular protein localization	PMID:15372076^[9]	ECO:0000315	mutant phenotype evidence used in manual assertion		P	has_input:(PomBase:SPAC6F12.09)	Seeded From UniProt	complete
involved_in	GO:0034613	cellular protein localization	PMID:15372076^[9]	ECO:0000315	mutant phenotype evidence used in manual assertion		P	has_input:(PomBase:SPAC18G6.02c)	Seeded From UniProt	complete
involved_in	GO:0034613	cellular protein localization	PMID:11283354^[4]	ECO:0000315	mutant phenotype evidence used in manual assertion		P	has_input:(PomBase:SPAC664.01c)	Seeded From UniProt	complete
part_of	GO:0031934	mating-type region heterochromatin	GO_REF:0000051	ECO:0000303	author statement without traceable support used in manual assertion		C		Seeded From UniProt	complete
involved_in	GO:0030702	chromatin silencing at centromere	PMID:7851795^[10]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0030466	chromatin silencing at silent mating-type cassette	PMID:8138176^[11]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0030466	chromatin silencing at silent mating-type cassette	PMID:8001791^[12]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0030466	chromatin silencing at silent mating-type cassette	PMID:11283354^[4]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0007535	donor selection	PMID:9620780^[13]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0006338	chromatin remodeling	GO_REF:0000051	ECO:0000303	author statement without traceable support used in manual assertion		P		Seeded From UniProt	complete
part_of	GO:0005634	nucleus	PMID:16823372^[14]	ECO:0007005	high throughput direct assay evidence used in manual assertion		C		Seeded From UniProt	complete
enables	GO:0003727	single-stranded RNA binding	PMID:22727667^[8]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0003697	single-stranded DNA binding	PMID:22727667^[8]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
enables	GO:0003690	double-stranded DNA binding	PMID:22727667^[8]	ECO:0000314	direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
involved_in	GO:0000183	chromatin silencing at rDNA	PMID:10835380^[15]	ECO:0000315	mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
involved_in	GO:0000122	negative regulation of transcription by RNA polymerase II	PMID:16407326^[16]	ECO:0000315	mutant phenotype evidence used in manual assertion		P	has_regulation_target:(PomBase:SPBCPT2R1.08c)	Seeded From UniProt	complete
involved_in	GO:0000122	negative regulation of transcription by RNA polymerase II	PMID:16407326^[16]	ECO:0000315	mutant phenotype evidence used in manual assertion		P	has_regulation_target:(PomBase:SPAC212.11)	Seeded From UniProt	complete
part_of	GO:0000781	chromosome, telomeric region	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0006348	C		Seeded From UniProt	complete
part_of	GO:0034507	chromosome, centromeric outer repeat region	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:1990141	C		Seeded From UniProt	complete
part_of	GO:0034507	chromosome, centromeric outer repeat region	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:1902368	C		Seeded From UniProt	complete
involved_in	GO:0051567	histone H3-K9 methylation	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0046974	P		Seeded From UniProt	complete
involved_in	GO:0051567	histone H3-K9 methylation	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0046974	P		Seeded From UniProt	complete
involved_in	GO:0051567	histone H3-K9 methylation	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0046974	P		Seeded From UniProt	complete
involved_in	GO:0051567	histone H3-K9 methylation	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0046974	P		Seeded From UniProt	complete
involved_in	GO:0051567	histone H3-K9 methylation	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0046974	P		Seeded From UniProt	complete
involved_in	GO:0051567	histone H3-K9 methylation	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0046974	P		Seeded From UniProt	complete
involved_in	GO:0051567	histone H3-K9 methylation	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0046974	P		Seeded From UniProt	complete
involved_in	GO:0051567	histone H3-K9 methylation	GO_REF:0000108	ECO:0000364	evidence based on logical inference from manual annotation used in automatic assertion	GO:0046974	P		Seeded From UniProt	complete
part_of	GO:0005634	nucleus	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR007728 InterPro:IPR011381	C		Seeded From UniProt	complete
enables	GO:0008270	zinc ion binding	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR007728	F		Seeded From UniProt	complete
enables	GO:0018024	histone-lysine N-methyltransferase activity	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR007728 InterPro:IPR011381	F		Seeded From UniProt	complete
involved_in	GO:0034968	histone lysine methylation	GO_REF:0000002	ECO:0000256	match to sequence model evidence used in automatic assertion	InterPro:IPR007728 InterPro:IPR011381	P		Seeded From UniProt	complete
enables	GO:0018024	histone-lysine N-methyltransferase activity	GO_REF:0000003	ECO:0000501	evidence used in automatic assertion	EC:2.1.1.43	F		Seeded From UniProt	complete
part_of	GO:0031618	nuclear pericentric heterochromatin	PMID:16127433^[7]	ECO:0000304	author statement supported by traceable reference used in manual assertion		C		Seeded From UniProt	complete
involved_in	GO:0006348	chromatin silencing at telomere	PMID:15197176^[6]	ECO:0000304	author statement supported by traceable reference used in manual assertion		P		Seeded From UniProt	complete
part_of	GO:0005737	cytoplasm	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0963	C		Seeded From UniProt	complete
involved_in	GO:0032259	methylation	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0489	P		Seeded From UniProt	complete
part_of	GO:0005634	nucleus	GO_REF:0000037 GO_REF:0000039	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0539 UniProtKB-SubCell:SL-0191	C		Seeded From UniProt	complete
involved_in	GO:0006325	chromatin organization	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0156	P		Seeded From UniProt	complete
enables	GO:0016740	transferase activity	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0808	F		Seeded From UniProt	complete
enables	GO:0046872	metal ion binding	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0479	F		Seeded From UniProt	complete
part_of	GO:0005694	chromosome	GO_REF:0000037 GO_REF:0000039	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0158 UniProtKB-SubCell:SL-0468	C		Seeded From UniProt	complete
enables	GO:0008168	methyltransferase activity	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0489	F		Seeded From UniProt	complete
part_of	GO:0005856	cytoskeleton	GO_REF:0000037	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-KW:KW-0206	C		Seeded From UniProt	complete
part_of	GO:0005816	spindle pole body	GO_REF:0000039	ECO:0000322	imported manually asserted information used in automatic assertion	UniProtKB-SubCell:SL-0252	C		Seeded From UniProt	complete
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Notes

References

See Help:References for how to manage references in GONUTS.

↑ Shimada, A et al. (2009) Phosphorylation of Swi6/HP1 regulates transcriptional gene silencing at heterochromatin. Genes Dev. 23 18-23 PubMed GONUTS page
↑ ^2.0 ^2.1 ^2.2 Tucker, JF et al. (2016) A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5'-3' Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe. PLoS Genet. 12 e1005873 PubMed GONUTS page
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 Rea, S et al. (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406 593-9 PubMed GONUTS page
↑ ^4.0 ^4.1 ^4.2 ^4.3 ^4.4 ^4.5 ^4.6 ^4.7 ^4.8 Nakayama, J et al. (2001) Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292 110-3 PubMed GONUTS page
↑ Alper, BJ et al. (2013) Sir2 is required for Clr4 to initiate centromeric heterochromatin assembly in fission yeast. EMBO J. 32 2321-35 PubMed GONUTS page
↑ ^6.0 ^6.1 Tuzon, CT et al. (2004) The fission yeast heterochromatin protein Rik1 is required for telomere clustering during meiosis. J. Cell Biol. 165 759-65 PubMed GONUTS page
↑ ^7.0 ^7.1 Jia, S et al. (2005) Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat. Cell Biol. 7 1007-13 PubMed GONUTS page
↑ ^8.0 ^8.1 ^8.2 ^8.3 Ishida, M et al. (2012) Intrinsic nucleic acid-binding activity of Chp1 chromodomain is required for heterochromatic gene silencing. Mol. Cell 47 228-41 PubMed GONUTS page
↑ ^9.0 ^9.1 ^9.2 Sadaie, M et al. (2004) A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J. 23 3825-35 PubMed GONUTS page
↑ Allshire, RC et al. (1995) Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9 218-33 PubMed GONUTS page
↑ Ekwall, K & Ruusala, T (1994) Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast. Genetics 136 53-64 PubMed GONUTS page
↑ Thon, G et al. (1994) Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe. Genetics 138 29-38 PubMed GONUTS page
↑ Ivanova, AV et al. (1998) The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast. Nat. Genet. 19 192-5 PubMed GONUTS page
↑ Matsuyama, A et al. (2006) ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat. Biotechnol. 24 841-7 PubMed GONUTS page
↑ Thon, G & Verhein-Hansen, J (2000) Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations. Genetics 155 551-68 PubMed GONUTS page
↑ ^16.0 ^16.1 Hansen, KR et al. (2006) Evolutionary-conserved telomere-linked helicase genes of fission yeast are repressed by silencing factors, RNAi components and the telomere-binding protein Taz1. Nucleic Acids Res. 34 78-88 PubMed GONUTS page

[PMID:19136623-1] Shimada, A et al. (2009) Phosphorylation of Swi6/HP1 regulates transcriptional gene silencing at heterochromatin. Genes Dev. 23 18-23 PubMed GONUTS page

[PMID:26889830-2] 2.0 ^2.1 ^2.2 Tucker, JF et al. (2016) A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5'-3' Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe. PLoS Genet. 12 e1005873 PubMed GONUTS page

[PMID:10949293-3] 3.0 ^3.1 ^3.2 ^3.3 ^3.4 Rea, S et al. (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406 593-9 PubMed GONUTS page

[PMID:11283354-4] 4.0 ^4.1 ^4.2 ^4.3 ^4.4 ^4.5 ^4.6 ^4.7 ^4.8 Nakayama, J et al. (2001) Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292 110-3 PubMed GONUTS page

[PMID:23771057-5] Alper, BJ et al. (2013) Sir2 is required for Clr4 to initiate centromeric heterochromatin assembly in fission yeast. EMBO J. 32 2321-35 PubMed GONUTS page

[PMID:15197176-6] 6.0 ^6.1 Tuzon, CT et al. (2004) The fission yeast heterochromatin protein Rik1 is required for telomere clustering during meiosis. J. Cell Biol. 165 759-65 PubMed GONUTS page

[PMID:16127433-7] 7.0 ^7.1 Jia, S et al. (2005) Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat. Cell Biol. 7 1007-13 PubMed GONUTS page

[PMID:22727667-8] 8.0 ^8.1 ^8.2 ^8.3 Ishida, M et al. (2012) Intrinsic nucleic acid-binding activity of Chp1 chromodomain is required for heterochromatic gene silencing. Mol. Cell 47 228-41 PubMed GONUTS page

[PMID:15372076-9] 9.0 ^9.1 ^9.2 Sadaie, M et al. (2004) A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J. 23 3825-35 PubMed GONUTS page

[PMID:7851795-10] Allshire, RC et al. (1995) Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9 218-33 PubMed GONUTS page

[PMID:8138176-11] Ekwall, K & Ruusala, T (1994) Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast. Genetics 136 53-64 PubMed GONUTS page

[PMID:8001791-12] Thon, G et al. (1994) Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe. Genetics 138 29-38 PubMed GONUTS page

[PMID:9620780-13] Ivanova, AV et al. (1998) The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast. Nat. Genet. 19 192-5 PubMed GONUTS page

[PMID:16823372-14] Matsuyama, A et al. (2006) ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat. Biotechnol. 24 841-7 PubMed GONUTS page

[PMID:10835380-15] Thon, G & Verhein-Hansen, J (2000) Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations. Genetics 155 551-68 PubMed GONUTS page

[PMID:16407326-16] 16.0 ^16.1 Hansen, KR et al. (2006) Evolutionary-conserved telomere-linked helicase genes of fission yeast are repressed by silencing factors, RNAi components and the telomere-binding protein Taz1. Nucleic Acids Res. 34 78-88 PubMed GONUTS page

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SCHPO:CLR4

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