GONUTS has been updated to MW1.29.2. Most things seem to be working but be sure to report problems.

It is now the 2nd CHALLENGE Period for CACAO Phage Hunters S2018! It will end on Monday July 16, 2018 at 05:59 pm CDT
This is your chance to challenge other team's annotations. You may also DEFEND or suggest improvements to your own annotations IF they have been challenged. Please note, although we ENCOURAGE challenges, an excess of identical challenges that do not appear to be applicable to the annotation or well thought out will be considered spam and ignored.

Have any questions? Please email us at ecoliwiki@gmail.com

SCHPO:CLR4

From GONUTS
Jump to: navigation, search
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
PDBsum 1G6Z
1MVH
1MVX
ProteinModelPortal O60016
SMR O60016
BioGrid 277343
DIP DIP-32588N
IntAct O60016
MINT MINT-195370
MaxQB O60016
EnsemblFungi [example_ID SPBC428.08c.1]
GeneID 2540825
KEGG spo:SPBC428.08c
EuPathDB FungiDB:SPBC428.08c
PomBase SPBC428.08c
InParanoid O60016
KO K11419
OrthoDB EOG7MD509
PhylomeDB O60016
Reactome R-SPO-3214841
EvolutionaryTrace O60016
NextBio 20801942
PRO PR:O60016
Proteomes UP000002485
GO GO:0034507
GO:0000781
GO:0043494
GO:0005737
GO:0031934
GO:0044732
GO:0031618
GO:1990707
GO:0005634
GO:0003690
GO:0042054
GO:0046974
GO:0035064
GO:0008168
GO:0003697
GO:0003727
GO:0008270
GO:0051315
GO:0034613
GO:0006338
GO:0030702
GO:1990141
GO:0000183
GO:0030466
GO:0006348
GO:0031048
GO:0007535
GO:1902368
GO:0051567
GO:0045141
GO:0000122
GO:0090065
GO:0032015
InterPro IPR000953
IPR023780
IPR016197
IPR023779
IPR011381
IPR003616
IPR007728
IPR003606
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 Evidence Code with/from Aspect Notes Status
GO:0000122

negative regulation of transcription from RNA polymerase II promoter

PMID:16407326[1]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0000122

negative regulation of transcription from RNA polymerase II promoter

PMID:16407326[1]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0000183

chromatin silencing at rDNA

PMID:10835380[2]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0000781

chromosome, telomeric region

PMID:15197176[3]

TAS: Traceable Author Statement

-

C

Seeded From UniProt

GO:0003690

double-stranded DNA binding

PMID:22727667[4]

IDA: Inferred from Direct Assay

-

F

Seeded From UniProt

GO:0003697

single-stranded DNA binding

PMID:22727667[4]

IDA: Inferred from Direct Assay

-

F

Seeded From UniProt

GO:0003727

single-stranded RNA binding

PMID:22727667[4]

IDA: Inferred from Direct Assay

-

F

Seeded From UniProt

GO:0005515

protein binding

PMID:16024659[5]

IPI: Inferred from Physical Interaction

UniProtKB:Q10426

F

Seeded From UniProt

GO:0005515

protein binding

PMID:16127433[6]

IPI: Inferred from Physical Interaction

UniProtKB:O14122

F

Seeded From UniProt

GO:0005515

protein binding

PMID:16127433[6]

IPI: Inferred from Physical Interaction

UniProtKB:Q10426

F

Seeded From UniProt

GO:0005515

protein binding

PMID:16168376[7]

IPI: Inferred from Physical Interaction

PomBase:SPAC30D11.13

F

Seeded From UniProt

GO:0005515

protein binding

PMID:20211136[8]

IPI: Inferred from Physical Interaction

UniProtKB:O94276

F

Seeded From UniProt

GO:0005634

nucleus

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003606
InterPro:IPR007728
InterPro:IPR011381

C

Seeded From UniProt

GO:0005634

nucleus

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0539

C

Seeded From UniProt

GO:0005634

nucleus

GO_REF:0000039

IEA: Inferred from Electronic Annotation

UniProtKB-SubCell:SL-0191

C

Seeded From UniProt

GO:0005634

nucleus

PMID:16823372[9]

IDA: Inferred from Direct Assay

-

C

Seeded From UniProt

GO:0005694

chromosome

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0158

C

Seeded From UniProt

GO:0005694

chromosome

GO_REF:0000039

IEA: Inferred from Electronic Annotation

UniProtKB-SubCell:SL-0468

C

Seeded From UniProt

GO:0005737

cytoplasm

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0963

C

Seeded From UniProt

GO:0005816

spindle pole body

GO_REF:0000039

IEA: Inferred from Electronic Annotation

UniProtKB-SubCell:SL-0252

C

Seeded From UniProt

GO:0005856

cytoskeleton

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0206

C

Seeded From UniProt

GO:0006338

chromatin remodeling

GO_REF:0000051

NAS: Non-traceable Author Statement

-

P

Seeded From UniProt

GO:0006348

chromatin silencing at telomere

PMID:15197176[3]

TAS: Traceable Author Statement

-

P

Seeded From UniProt

GO:0007535

donor selection

PMID:9620780[10]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0008168

methyltransferase activity

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0489

F

Seeded From UniProt

GO:0008168

methyltransferase activity

PMID:10949293[11]

IDA: Inferred from Direct Assay

-

F

Seeded From UniProt

GO:0008270

zinc ion binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003606
InterPro:IPR007728

F

Seeded From UniProt

GO:0016568

chromatin modification

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0156

P

Seeded From UniProt

GO:0016740

transferase activity

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0808

F

Seeded From UniProt

GO:0018024

histone-lysine N-methyltransferase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003606
InterPro:IPR007728
InterPro:IPR011381

F

Seeded From UniProt

GO:0018024

histone-lysine N-methyltransferase activity

GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.1.1.43

F

Seeded From UniProt

GO:0030466

chromatin silencing at silent mating-type cassette

PMID:8001791[12]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0030466

chromatin silencing at silent mating-type cassette

PMID:8138176[13]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0030702

chromatin silencing at centromere

PMID:7851795[14]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0031048

chromatin silencing by small RNA

PMID:12869699[15]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0031618

nuclear pericentric heterochromatin

PMID:16127433[6]

TAS: Traceable Author Statement

-

C

Seeded From UniProt

GO:0031934

mating-type region heterochromatin

GO_REF:0000001

NAS: Non-traceable Author Statement

-

C

Seeded From UniProt

GO:0032015

regulation of Ran protein signal transduction

PMID:18422602[16]

TAS: Traceable Author Statement

-

P

Seeded From UniProt

GO:0032259

methylation

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0489

P

Seeded From UniProt

GO:0034507

chromosome, centromeric outer repeat region

PMID:23771057[17]

IGI: Inferred from Genetic Interaction

PomBase:SPBC16D10.07c

C

Seeded From UniProt

GO:0034507

chromosome, centromeric outer repeat region

PMID:25274039[18]

IMP: Inferred from Mutant Phenotype

-

C

Seeded From UniProt

GO:0034613

cellular protein localization

PMID:11283354[19]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0034613

cellular protein localization

PMID:15372076[20]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0034613

cellular protein localization

PMID:15372076[20]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0034613

cellular protein localization

PMID:15372076[20]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0034968

histone lysine methylation

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003606
InterPro:IPR007728
InterPro:IPR011381

P

Seeded From UniProt

GO:0035064

methylated histone binding

PMID:22727667[4]

IDA: Inferred from Direct Assay

-

F

Seeded From UniProt

GO:0042054

histone methyltransferase activity

PMID:25774602[21]

IDA: Inferred from Direct Assay

-

F

Seeded From UniProt

GO:0043494

CLRC ubiquitin ligase complex

PMID:16127433[6]

IDA: Inferred from Direct Assay

-

C

Seeded From UniProt

GO:0044732

mitotic spindle pole body

PMID:16823372[9]

IDA: Inferred from Direct Assay

-

C

Seeded From UniProt

GO:0045141

meiotic telomere clustering

PMID:15197176[3]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0046872

metal ion binding

GO_REF:0000037

IEA: Inferred from Electronic Annotation

UniProtKB-KW:KW-0479

F

Seeded From UniProt

GO:0046974

histone methyltransferase activity (H3-K9 specific)

PMID:10949293[11]

IDA: Inferred from Direct Assay

-

F

Seeded From UniProt

GO:0046974

histone methyltransferase activity (H3-K9 specific)

PMID:10949293[11]

IDA: Inferred from Direct Assay

-

F

Seeded From UniProt

GO:0051315

attachment of mitotic spindle microtubules to kinetochore

PMID:17627824[22]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:0051567

histone H3-K9 methylation

PMID:10949293[11]

IDA: Inferred from Direct Assay

-

P

Seeded From UniProt

GO:0090065

regulation of production of siRNA involved in RNA interference

PMID:12869699[15]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:1902368

heterochromatin maintenance involved in chromatin silencing at centromere outer repeat region

PMID:23771057[17]

IGI: Inferred from Genetic Interaction

PomBase:SPBC16D10.07c

P

Seeded From UniProt

GO:1990141

chromatin silencing at centromere outer repeat region

PMID:25274039[18]

IMP: Inferred from Mutant Phenotype

-

P

Seeded From UniProt

GO:1990707

nuclear subtelomeric heterochromatin

GO_REF:0000001

NAS: Non-traceable Author Statement

-

C

Seeded From UniProt

GO:0090053

positive regulation of chromatin silencing at centromere

PMID:19136623[23]

IMP: Inferred from Mutant Phenotype

P

silencing defects in ckb1Δ cells was comparable with that caused by disruption of other heterochromatic genes, including clr4,Fig. 1B).

complete

GO:0030702

chromatin silencing at centromere

PMID:26889830[24]

IMP: Inferred from Mutant Phenotype

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[24]

IMP: Inferred from Mutant Phenotype

P

Figure 2A

complete
CACAO 11329

GO:1900111

positive regulation of histone H3-K9 dimethylation

PMID:26889830[24]

IMP: Inferred from Mutant Phenotype

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

Notes

References

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

  1. 1.0 1.1 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
  2. 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
  3. 3.0 3.1 3.2 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
  4. 4.0 4.1 4.2 4.3 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
  5. Horn, PJ et al. (2005) A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev. 19 1705-14 PubMed GONUTS page
  6. 6.0 6.1 6.2 6.3 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
  7. Shin, JA et al. (2005) SUMO modification is involved in the maintenance of heterochromatin stability in fission yeast. Mol. Cell 19 817-28 PubMed GONUTS page
  8. Bayne, EH et al. (2010) Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell 140 666-77 PubMed GONUTS page
  9. 9.0 9.1 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
  10. 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
  11. 11.0 11.1 11.2 11.3 Rea, S et al. (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406 593-9 PubMed GONUTS page
  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
  13. 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
  14. Allshire, RC et al. (1995) Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9 218-33 PubMed GONUTS page
  15. 15.0 15.1 Schramke, V & Allshire, R (2003) Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301 1069-74 PubMed GONUTS page
  16. Ohba, T et al. (2008) Schizosaccharomyces pombe Snf2SR, a novel SNF2 family protein, interacts with Ran GTPase and modulates both RanGEF and RanGAP activities. Genes Cells 13 571-82 PubMed GONUTS page
  17. 17.0 17.1 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
  18. 18.0 18.1 Bayne, EH et al. (2014) A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast. Genome Biol. 15 481 PubMed GONUTS page
  19. 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
  20. 20.0 20.1 20.2 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
  21. Wang, J et al. (2015) Rapid epigenetic adaptation to uncontrolled heterochromatin spreading. Elife 4 PubMed GONUTS page
  22. Gregan, J et al. (2007) The kinetochore proteins Pcs1 and Mde4 and heterochromatin are required to prevent merotelic orientation. Curr. Biol. 17 1190-200 PubMed GONUTS page
  23. Shimada, A et al. (2009) Phosphorylation of Swi6/HP1 regulates transcriptional gene silencing at heterochromatin. Genes Dev. 23 18-23 PubMed GONUTS page
  24. 24.0 24.1 24.2 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