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protein coding gene - msc1 (SPAC343.11c) - Swr1 complex histone demethylase subunit Msc1

Gene summary

Standard name
msc1
Systematic ID
SPAC343.11c
Product
Swr1 complex histone demethylase subunit Msc1
Organism
Schizosaccharomyces pombe (fission yeast)
UniProt ID
Q9UT79
ORFeome ID
31/31A04
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 1658316..1663315 reverse strand

Annotation

Disease association

MONDO:0970951 - El Hayek-Chahrour neurodevelopmental disorder

References:

MONDO:0020850 - intellectual disability, autosomal recessive 65

References:

MONDO:0010355 - syndromic X-linked intellectual disability Claes-Jensen type

References:

GO biological process

GO:0006338 - chromatin remodeling

References:

GO:0070828 - heterochromatin organization

References:

GO:0007533 - mating type switching

References:

GO:0045815 - transcription initiation-coupled chromatin remodeling

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GO cellular component

GO:0000785 - chromatin

References:

GO:0000118 - histone deacetylase complex

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GO:0000812 - Swr1 complex

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GO molecular function

GO:0032452 - histone demethylase activity

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Modification

MOD:00046 - O-phospho-L-serine

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MOD:00047 - O-phospho-L-threonine

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

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MOD:01149 - sumoylated lysine

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Multi-locus phenotype

FYPO:0000082 - decreased cell population growth at high temperature

References:

Genotypes:

FYPO:0000080 - decreased cell population growth at low temperature

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Genotypes:

FYPO:0003743 - decreased cell population growth during glucose starvation

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Genotypes:

FYPO:0001407 - decreased cell population growth on glucose carbon source

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Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

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Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

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Genotypes:

FYPO:0004377 - increased protein localization to heterochromatin at silent mating-type cassette

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0000674 - normal cell population growth at high temperature

References:

Genotypes:

FYPO:0002141 - normal cell population growth at low temperature

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Genotypes:

FYPO:0001164 - normal growth on glucose carbon source

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Genotypes:

FYPO:0000472 - normal mating type switching

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Genotypes:

FYPO:0003503 - normal vegetative cell length

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Genotypes:

FYPO:0001357 - normal vegetative cell population growth

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Genotypes:

FYPO:0000091 - sensitive to thiabendazole

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Genotypes:

FYPO:0002546 - sensitive to trichostatin A

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Genotypes:

FYPO:0003241 - unequal mitotic sister chromatid segregation

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Genotypes:

FYPO:0002060 - viable vegetative cell population

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Genotypes:

Protein features

PBO:0111833 - jmjC domain

PBO:0111834 - jmjN domain

PBO:0111832 - zf-C5HC2 type

PBO:0111780 - zf-PHD finger

PBO:0111743 - zinc finger protein

Qualitative gene expression

PomGeneEx:0000026 - ribosomal density increased

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PomGeneEx:0000011 - RNA level increased

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Quantitative gene expression

PBO:0006310 - protein level

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PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0000051 - abnormal meiosis

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Genotypes:

FYPO:0002488 - cell lysis

References:

Genotypes:

FYPO:0000227 - chromosome loss during mitotic chromosome segregation

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Genotypes:

FYPO:0003743 - decreased cell population growth during glucose starvation

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Genotypes:

FYPO:0009053 - decreased cell population growth on glutamate nitrogen source

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Genotypes:

FYPO:0009091 - decreased cell population growth on lysine and proline nitrogen source

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Genotypes:

FYPO:0009092 - decreased cell population growth on lysine and serine nitrogen source

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Genotypes:

FYPO:0009073 - decreased cell population growth on lysine nitrogen source

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Genotypes:

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

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Genotypes:

FYPO:0007562 - decreased cell population growth on serine nitrogen source

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Genotypes:

FYPO:0002827 - decreased chromatin silencing at silent mating-type cassette

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Genotypes:

FYPO:0000884 - decreased histone H3-K9 trimethylation at centromere inner repeat during vegetative growth

References:

Genotypes:

FYPO:0000470 - decreased mating type switching

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Genotypes:

FYPO:0000450 - decreased protein localization to centromere during vegetative growth

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Genotypes:

FYPO:0002909 - decreased protein localization to chromatin during vegetative growth

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Genotypes:

FYPO:0003573 - decreased protein localization to heterochromatin at silent mating-type cassette

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Genotypes:

FYPO:0005749 - decreased protein phosphorylation during glucose starvation

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Genotypes:

FYPO:0003938 - increased cell population growth during glucose starvation

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Genotypes:

FYPO:0009077 - increased cell population growth on ethanol carbon source

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Genotypes:

FYPO:0004167 - increased cell population growth on glycerol carbon source

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Genotypes:

FYPO:0005071 - increased chromatin silencing at centromere

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Genotypes:

FYPO:0006299 - increased chromatin silencing at centromere outer repeat

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Genotypes:

FYPO:0000875 - increased histone H3-K9 dimethylation at centromere inner repeat during vegetative growth

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Genotypes:

FYPO:0000887 - increased histone H3-K9 dimethylation at centromere outer repeat during vegetative growth

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Genotypes:

FYPO:0000451 - increased protein localization to centromere during vegetative growth

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Genotypes:

FYPO:0004237 - increased protein localization to heterochromatin at centromere outer repeat region

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Genotypes:

FYPO:0004380 - increased protein localization to pericentric heterochromatin during vegetative growth

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Genotypes:

FYPO:0004557 - increased vegetative cell population growth

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Genotypes:

FYPO:0001309 - increased viability in stationary phase

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Genotypes:

FYPO:0000674 - normal cell population growth at high temperature

References:

Genotypes:

FYPO:0002141 - normal cell population growth at low temperature

References:

Genotypes:

FYPO:0002335 - normal chromatin silencing

References:

Genotypes:

FYPO:0002620 - normal growth on trichostatin A

References:

Genotypes:

FYPO:0000863 - normal histone H3-K9 dimethylation at centromere inner repeat during vegetative growth

References:

Genotypes:

FYPO:0008203 - normal histone H3-K9 trimethylation at centromere inner repeat during vegetative growth

References:

Genotypes:

FYPO:0000833 - normal protein level during vegetative growth

References:

Genotypes:

FYPO:0008154 - normal protein localization to centromeric heterochromatin

References:

Genotypes:

FYPO:0001317 - normal RNA level during vegetative growth

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0000067 - resistance to brefeldin A

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Genotypes:

FYPO:0009079 - resistance to calcofluor and sodium dodecyl sulfate

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Genotypes:

FYPO:0002693 - resistance to diamide

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Genotypes:

FYPO:0009034 - resistance to ethylenediaminetetraacetic acid

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Genotypes:

FYPO:0002578 - resistance to hydroxyurea

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Genotypes:

FYPO:0009085 - resistance to lithium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0002767 - resistance to terbinafine

References:

Genotypes:

FYPO:0003383 - resistance to tert-butyl hydroperoxide

References:

Genotypes:

FYPO:0000069 - resistance to thiabendazole

References:

Genotypes:

FYPO:0005193 - resistance to torin1

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Genotypes:

FYPO:0007808 - resistance to valproic acid

References:

Genotypes:

FYPO:0000830 - resistance to vanadate

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Genotypes:

FYPO:0000096 - sensitive to cadmium

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Genotypes:

FYPO:0000104 - sensitive to cycloheximide

References:

Genotypes:

FYPO:0000842 - sensitive to ethanol during vegetative growth

References:

Genotypes:

FYPO:0000785 - sensitive to formamide

References:

Genotypes:

FYPO:0001719 - sensitive to lithium

References:

Genotypes:

FYPO:0007924 - sensitive to potassium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0001457 - sensitive to tunicamycin

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
PF02373JmjCJmjC_domPFAM
PF00628PHDZnf_PHD-fingerPFAM
PF02928zf-C5HC2Znf_C5HC2PFAM
PF08429PLU-1Lys_sp_deMease-like_domPFAM
cd15489PHD_SFCDD
cd15518PHD_Ecm5p_Lid2p_likeCDD
PS01359ZF_PHD_1Zinc_finger_PHD-type_CSPROSITE_PATTERNS
PS51184JMJCJmjC_domPROSITE_PROFILES
PS50016ZF_PHD_2Znf_PHD-fingerPROSITE_PROFILES
PS51183JMJNJmjNPROSITE_PROFILES
SM00558cupin_9JmjC_domSMART
SM00545JmjN_1JmjNSMART
SM00249PHD_3Znf_PHDSMART
G3DSA:3.30.40.10:FF:001132FUNFAM
SSF57903FYVE/PHD zinc fingerZnf_FYVE_PHDSUPERFAMILY
SSF51197Clavaminate synthase-likeSUPERFAMILY
G3DSA:2.60.120.650CupinGENE3D
G3DSA:3.30.40.10Zinc/RING finger domain, C3HC4 (zinc finger)Znf_RING/FYVE/PHDGENE3D
PTHR10694LYSINE-SPECIFIC DEMETHYLASEPANTHER
CoilCoilCOILS
mobidb-lite-Disorderdisorder_predictionMOBIDB-Disorder
mobidb-lite-Polardisorder_predictionMOBIDB-Polar

Orthologs

References / Literature

PMID:19040720 - Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.
Shevchenko A et al. Genome Biol 2008;9(11):R167
PMID:19915592 - An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.
Kim HS et al. Nat Struct Mol Biol 2009 Dec;16(12):1286-93
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: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: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:32269268 - Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin.
Dong W et al. Sci Rep 2020 Apr 08;10(1):6055
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:34250083 - Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast.
Romila CA et al. Microb Cell 2021 Jul 05;8(7):146-160
PMID:28600551 - Epe1 contributes to activation of AMPK by promoting phosphorylation of AMPK alpha subunit, Ssp2.
Chen Y et al. Sci Rep 2017 Jun 09;7(1):3208
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:18505873 - Schizosaccharomyces pombe histone acetyltransferase Mst1 (KAT5) is an essential protein required for damage response and chromosome segregation.
Gómez EB et al. Genetics 2008 Jun;179(2):757-71
PMID:17947424 - Msc1 acts through histone H2A.Z to promote chromosome stability in Schizosaccharomyces pombe.
Ahmed S et al. Genetics 2007 Nov;177(3):1487-97
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:12161753 - The transcriptional program of meiosis and sporulation in fission yeast.
Mata J et al. Nat Genet 2002 Sep;32(1):143-7
PMID:28827290 - Kinetochore Components Required for Centromeric Chromatin Assembly Are Impacted by Msc1 in Schizosaccharomyces pombe .
Gao C et al. Genetics 2017 Oct;207(2):559-569
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: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:19693008 - Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs.
Zofall M et al. Nature 2009 Sep 17;461(7262):419-22
GO_REF:0000111 - Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference
PMID:33313903 - Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.
Rubio A et al. Nucleic Acids Res 2021 Jan 11;49(1):383-399
PMID:19911051 - The Schizosaccharomyces pombe JmjC-protein, Msc1, prevents H2A.Z localization in centromeric and subtelomeric chromatin domains.
Buchanan L et al. PLoS Genet 2009 Nov;5(11):e1000726
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: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
PMID:26537787 - Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast.
Køhler JB et al. Nat Commun 2015 Nov 05;6:8827
PMID:15082762 - A novel protein with similarities to Rb binding protein 2 compensates for loss of Chk1 function and affects histone modification in fission yeast.
Ahmed S et al. Mol Cell Biol 2004 May;24(9):3660-9
PMID:24957674 - Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts.
Anver S et al. EMBO Rep 2014 Aug;15(8):894-902
PMID:25838386 - Epigenetics. Restricted epigenetic inheritance of H3K9 methylation.
Audergon PN et al. Science 2015 Apr 03;348(6230):132-5
PMID:26404184 - High Confidence Fission Yeast SUMO Conjugates Identified by Tandem Denaturing Affinity Purification.
Nie M et al. Sci Rep 2015 Sep 25;5:14389
PMID:28410370 - A systematic screen for morphological abnormalities during fission yeast sexual reproduction identifies a mechanism of actin aster formation for cell fusion.
Dudin O et al. PLoS Genet 2017 Apr;13(4):e1006721
PMID:19164572 - Msc1 links dynamic Swi6/HP1 binding to cell fate determination.
Lawrence RJ et al. Proc Natl Acad Sci U S A 2009 Jan 27;106(4):1163-8
PMID:22540037 - Predicting the fission yeast protein interaction network.
Pancaldi V et al. G3 (Bethesda) 2012 Apr;2(4):453-67
PMID:17456468 - The plant homeodomain fingers of fission yeast Msc1 exhibit E3 ubiquitin ligase activity.
Dul BE et al. J Biol Chem 2007 Jun 22;282(25):18397-18406
PMID:20858896 - Activity of a C-terminal plant homeodomain (PHD) of Msc1 is essential for function.
Qiu X et al. J Biol Chem 2010 Nov 19;285(47):36828-35
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
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: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:19910462 - Histone variant H2A.Z regulates centromere silencing and chromosome segregation in fission yeast.
Hou H et al. J Biol Chem 2010 Jan 15;285(3):1909-18
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:16169489 - Novel genes required for meiotic chromosome segregation are identified by a high-throughput knockout screen in fission yeast.
Gregan J et al. Curr Biol 2005 Sep 20;15(18):1663-9
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:23695164 - Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways.
Das J et al. Sci Signal 2013 May 21;6(276):ra38
PMID:26510788 - Escape from Mitotic Arrest: An Unexpected Connection Between Microtubule Dynamics and Epigenetic Regulation of Centromeric Chromatin in Schizosaccharomyces pombe.
George AA et al. Genetics 2015 Dec;201(4):1467-78