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protein coding gene - set9 (SPCC4B3.12) - histone lysine H4-K20 methyltransferase Set9

Gene summary

Standard name
set9
Systematic ID
SPCC4B3.12
Product
histone lysine H4-K20 methyltransferase Set9
Organism
Schizosaccharomyces pombe (fission yeast)
UniProt ID
Q9USK2
ORFeome ID
23/23A10
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome III: 1153914..1156061 reverse strand

Annotation

Comment

PBO:0000206 - deletion mutant expression profiling

References:

Disease association

MONDO:0030917 - intellectual disability, autosomal dominant 51

References:

GO biological process

GO:0006338 - chromatin remodeling

References:

GO:0007095 - mitotic G2 DNA damage checkpoint signaling

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GO:0006289 - nucleotide-excision repair

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GO:0031508 - pericentric heterochromatin formation

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GO:0010468 - regulation of gene expression

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GO cellular component

GO:0032153 - cell division site

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GO:0000785 - chromatin

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GO:0005829 - cytosol

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GO:0044732 - mitotic spindle pole body

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GO:0005634 - nucleus

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GO molecular function

GO:0042393 - histone binding

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GO:0140943 - histone H4K20 trimethyltransferase activity

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GO:0031491 - nucleosome binding

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Multi-locus phenotype

FYPO:0003081 - decreased genetic imprinting at mating-type locus

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Genotypes:

FYPO:0004372 - decreased response to mitotic G2 DNA damage checkpoint signaling

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Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

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Genotypes:

FYPO:0002554 - normal protein localization to double-strand break site

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Genotypes:

FYPO:0000085 - sensitive to camptothecin

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Genotypes:

FYPO:0000265 - sensitive to DNA damage

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Genotypes:

FYPO:0000267 - sensitive to ionizing radiation during vegetative growth

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Genotypes:

FYPO:0000268 - sensitive to UV during vegetative growth

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Genotypes:

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

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Genotypes:

Protein features

PBO:0111852 - SET domain

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

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Quantitative gene expression

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0002900 - abnormal mitotic DNA damage checkpoint during cellular response to UV

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Genotypes:

FYPO:0004217 - abolished histone H4-K20 dimethylation during vegetative growth

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Genotypes:

FYPO:0004216 - abolished histone H4-K20 monomethylation during vegetative growth

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Genotypes:

FYPO:0004218 - abolished histone H4-K20 trimethylation during vegetative growth

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Genotypes:

FYPO:0004232 - abolished methylated histone binding

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Genotypes:

FYPO:0002898 - abolished protein phosphorylation during cellular response to DNA damage

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Genotypes:

FYPO:0002471 - abolished protein phosphorylation during cellular response to ionizing radiation

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Genotypes:

FYPO:0008179 - decreased histone H4-K20 monomethylation during vegetative growth

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Genotypes:

FYPO:0004224 - decreased histone H4-K20 trimethylation during vegetative growth

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Genotypes:

FYPO:0007272 - decreased protein localization to nucleoplasm during cellular response to DNA damage

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Genotypes:

FYPO:0002897 - decreased protein phosphorylation during cellular response to DNA damage

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Genotypes:

FYPO:0004228 - decreased protein phosphorylation during cellular response to UV

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Genotypes:

FYPO:0004372 - decreased response to mitotic G2 DNA damage checkpoint signaling

References:

Genotypes:

FYPO:0009008 - increased vegetative cell population viability

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Genotypes:

FYPO:0004344 - increased viability upon nitrogen starvation

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Genotypes:

FYPO:0003082 - normal genetic imprinting at mating-type locus

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Genotypes:

FYPO:0001690 - normal growth on camptothecin

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Genotypes:

FYPO:0001164 - normal growth on glucose carbon source

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Genotypes:

FYPO:0000964 - normal growth on thiabendazole

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Genotypes:

FYPO:0002601 - normal histone H2A phosphorylation during vegetative growth

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Genotypes:

FYPO:0003132 - normal punctate nuclear localization during cellular response to ionizing radiation

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Genotypes:

FYPO:0000441 - resistance to antimycin A

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Genotypes:

FYPO:0009032 - resistance to bortezomib

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Genotypes:

FYPO:0000067 - resistance to brefeldin A

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Genotypes:

FYPO:0000764 - resistance to cycloheximide

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Genotypes:

FYPO:0002693 - resistance to diamide

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Genotypes:

FYPO:0009047 - resistance to dimethyl sulfoxide

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Genotypes:

FYPO:0009038 - resistance to egtazic acid

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Genotypes:

FYPO:0001453 - resistance to ethanol

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Genotypes:

FYPO:0009035 - resistance to formamide

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Genotypes:

FYPO:0009087 - resistance to magnesium chloride and sodium dodecyl sulfate

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Genotypes:

FYPO:0000725 - resistance to methyl methanesulfonate

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Genotypes:

FYPO:0009039 - resistance to potassium chloride

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Genotypes:

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

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Genotypes:

FYPO:0000077 - resistance to rapamycin

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Genotypes:

FYPO:0009042 - resistance to sorbitol

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Genotypes:

FYPO:0002767 - resistance to terbinafine

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Genotypes:

FYPO:0003383 - resistance to tert-butyl hydroperoxide

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Genotypes:

FYPO:0000830 - resistance to vanadate

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Genotypes:

FYPO:0000095 - sensitive to bleomycin

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Genotypes:

FYPO:0000085 - sensitive to camptothecin

References:

Genotypes:

FYPO:0000265 - sensitive to DNA damage

References:

Genotypes:

FYPO:0000267 - sensitive to ionizing radiation during vegetative growth

References:

Genotypes:

FYPO:0009084 - sensitive to lithium chloride and methyl methanesulfonate

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Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

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Genotypes:

FYPO:0009082 - sensitive to potassium chloride and methyl methanesulfonate

References:

Genotypes:

FYPO:0007925 - sensitive to sodium chloride and methyl methanesulfonate

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Genotypes:

FYPO:0000268 - sensitive to UV during vegetative growth

References:

Genotypes:

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

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

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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
PF00856SETSET_domPfam
cd10524SET_Suv4-20-likeCDD
PS50280SETSET_domPROSITE profiles
PS51567SAM_MT43_SUVAR420_1Set9_fungiPROSITE profiles
SM00317SETSET_domSMART
G3DSA:1.10.10.1700:FF:000001CATH-FunFam
G3DSA:1.10.10.1700Hist-Lys_N-MTase_NCATH-Gene3D
G3DSA:2.170.270.10SET_dom_sfCATH-Gene3D
SSF82199SET_dom_sfSUPERFAMILY
PTHR12977Suv4-20/Set9PANTHER

Orthologs

References / Literature

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:16778077 - Histone modification-dependent and -independent pathways for recruitment of checkpoint protein Crb2 to double-strand breaks.
Du LL et al. Genes Dev 2006 Jun 15;20(12):1583-96
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:24806815 - Mdb1, a fission yeast homolog of human MDC1, modulates DNA damage response and mitotic spindle function.
Wei Y et al. PLoS One 2014;9(5):e97028
PMID:19250904 - Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein.
Wang Y et al. Mol Cell 2009 Feb 27;33(4):428-37
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: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:26205977 - Highly condensed chromatins are formed adjacent to subtelomeric and decondensed silent chromatin in fission yeast.
Matsuda A et al. Nat Commun 2015 Jul 24;6:7753
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:18931302 - Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes.
Dixon SJ et al. Proc Natl Acad Sci U S A 2008 Oct 28;105(43):16653-8
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:27098497 - CRL4(Wdr70) regulates H2B monoubiquitination and facilitates Exo1-dependent resection.
Zeng M et al. Nat Commun 2016 Apr 21;7:11364
PMID:27268234 - Both H4K20 mono-methylation and H3K56 acetylation mark transcription-dependent histone turnover in fission yeast.
Yang H et al. Biochem Biophys Res Commun 2016 Aug 05;476(4):515-521
PMID:17434129 - S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription.
Lan F et al. Mol Cell 2007 Apr 13;26(1):89-101
PMID:34984977 - Functional profiling of long intergenic non-coding RNAs in fission yeast.
Rodriguez-Lopez M et al. Elife 2022 Jan 05;11
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:39367033 - Quantitative proteomics and phosphoproteomics profiling of meiotic divisions in the fission yeast Schizosaccharomyces pombe.
Sivakova B et al. Sci Rep 2024 Oct 04;14(1):23105
PMID:25452419 - Parallel profiling of fission yeast deletion mutants for proliferation and for lifespan during long-term quiescence.
Sideri T et al. G3 (Bethesda) 2014 Dec 01;5(1):145-55
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:23260662 - Lsd1 and lsd2 control programmed replication fork pauses and imprinting in fission yeast.
Holmes A et al. Cell Rep 2012 Dec 27;2(6):1513-20
PMID:28357272 - A central role for TOR signalling in a yeast model for juvenile CLN3 disease.
Bond ME et al. Microb Cell 2015 Nov 11;2(12):466-480
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:26368543 - Critical Function of γH2A in S-Phase.
Mejia-Ramirez E et al. PLoS Genet 2015 Sep;11(9):e1005517
PMID:15550243 - Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage.
Sanders SL et al. Cell 2004 Nov 24;119(5):603-14