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protein coding gene - mit1 (SPBP35G2.10) - SHREC complex ATP-dependent chromatin remodeller Mit1

Gene summary

Standard name
mit1
Systematic ID
SPBP35G2.10
Product
SHREC complex ATP-dependent chromatin remodeller Mit1
Organism
Schizosaccharomyces pombe (fission yeast)
UniProt ID
Q9P793
ORFeome ID
39/39E04
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 982068..986422 forward strand

Annotation

Disease association

MONDO:0859249 - parenti-mignot neurodevelopmental syndrome

References:

MONDO:0014946 - Sifrim-Hitz-Weiss syndrome

References:

MONDO:0032600 - Snijders Blok-Campeau syndrome

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GO biological process

GO:0006325 - chromatin organization

References:

GO:0006338 - chromatin remodeling

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GO:0031508 - pericentric heterochromatin formation

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GO:0000183 - rDNA heterochromatin formation

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GO:0030466 - silent mating-type cassette heterochromatin formation

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GO:0031509 - subtelomeric heterochromatin formation

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GO cellular component

GO:1990342 - heterochromatin island

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GO:0031934 - mating-type region heterochromatin

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GO:0005634 - nucleus

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GO:0005721 - pericentric heterochromatin

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GO:0033553 - rDNA heterochromatin

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GO:0070824 - SHREC complex

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GO:0140720 - subtelomeric heterochromatin

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GO molecular function

GO:0005524 - ATP binding

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GO:0016887 - ATP hydrolysis activity

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GO:0003677 - DNA binding

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GO:0042393 - histone binding

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GO:0140750 - nucleosome array spacer activity

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GO:0031491 - nucleosome binding

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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:0004170 - abolished histone H3-K9 dimethylation at centromere during vegetative growth

References:

Genotypes:

FYPO:0008153 - abolished protein localization to heterochromatin at silent mating-type cassette during vegetative growth

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Genotypes:

FYPO:0006993 - decreased chromatin silencing at centromere otr1R

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Genotypes:

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

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Genotypes:

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

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Genotypes:

FYPO:0002386 - decreased protein localization to pericentric heterochromatin at centromere outer repeat region

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Genotypes:

FYPO:0002019 - elongated telomeres during vegetative growth

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Genotypes:

FYPO:0000220 - increased centromeric outer repeat transcript level

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Genotypes:

FYPO:0005917 - increased subtelomeric heterochromatin RNA level

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Genotypes:

FYPO:0002336 - normal chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0000091 - sensitive to thiabendazole

References:

Genotypes:

Protein features

PBO:0111747 - DEAD/DEAH box helicase

PBO:0111780 - zf-PHD finger

PBO:0111743 - zinc finger protein

Qualitative gene expression

PomGeneEx:0000018 - protein level increased

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Quantitative gene expression

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0000121 - abnormal sporulation

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Genotypes:

FYPO:0003674 - abolished ATPase activity

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Genotypes:

FYPO:0007336 - abolished chromatin silencing at silent mating-type cassette

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Genotypes:

FYPO:0003094 - decreased centromeric outer repeat transcript level

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Genotypes:

FYPO:0005929 - decreased chromatin binding at centromere outer repeat

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Genotypes:

FYPO:0003411 - decreased chromatin silencing at centromere inner repeat

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Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

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Genotypes:

FYPO:0003216 - decreased chromatin silencing at rDNA

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Genotypes:

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

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Genotypes:

FYPO:0004604 - decreased chromatin silencing at subtelomere

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Genotypes:

FYPO:0005931 - decreased nucleosome occupancy at silent mating-type cassette

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Genotypes:

FYPO:0008341 - decreased nucleosome occupancy in gene body

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Genotypes:

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

References:

Genotypes:

FYPO:0002386 - decreased protein localization to pericentric heterochromatin at centromere outer repeat region

References:

Genotypes:

FYPO:0001117 - decreased RNA level during vegetative growth

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Genotypes:

FYPO:0002019 - elongated telomeres during vegetative growth

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Genotypes:

FYPO:0004806 - incomplete cell wall disassembly at cell fusion site

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Genotypes:

FYPO:0000220 - increased centromeric outer repeat transcript level

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Genotypes:

FYPO:0002836 - increased centromeric outer repeat transcript-derived siRNA level

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Genotypes:

FYPO:0000966 - increased histone H3-K14 acetylation at centromere outer repeat during vegetative growth

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Genotypes:

FYPO:0006681 - increased histone H3-K9 acetylation at centromere inner repeat during vegetative growth

References:

Genotypes:

FYPO:0003011 - increased protein localization to chromatin during vegetative growth

References:

Genotypes:

FYPO:0006300 - increased protein localization to heterochromatin at centromere inner repeat

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Genotypes:

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

References:

Genotypes:

FYPO:0000825 - increased RNA level during vegetative growth

References:

Genotypes:

FYPO:0005917 - increased subtelomeric heterochromatin RNA level

References:

Genotypes:

FYPO:0006518 - loss of viability in G0

References:

Genotypes:

FYPO:0002567 - normal centromeric outer repeat transcript level

References:

Genotypes:

FYPO:0005930 - normal chromatin binding at centromere outer repeat

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Genotypes:

FYPO:0002336 - normal chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0007553 - normal G1 to G0 transition

References:

Genotypes:

FYPO:0003235 - normal histone H3-K9 methylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0005865 - normal histone H3-K9 methylation at silent mating-type cassette during vegetative growth

References:

Genotypes:

FYPO:0005864 - normal histone H3-K9 methylation at subtelomeric heterochromatin during vegetative growth

References:

Genotypes:

FYPO:0002390 - normal mitotic sister chromatid cohesion

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Genotypes:

FYPO:0000857 - normal nucleosome positioning in euchromatin

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Genotypes:

FYPO:0006163 - normal protein localization to chromatin

References:

Genotypes:

FYPO:0000703 - normal protein-protein interaction

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Genotypes:

FYPO:0006014 - promiscuous mating

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Genotypes:

FYPO:0009036 - resistance to benzamidine

References:

Genotypes:

FYPO:0000763 - resistance to cadmium

References:

Genotypes:

FYPO:0000073 - resistance to caffeine

References:

Genotypes:

FYPO:0000764 - resistance to cycloheximide

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Genotypes:

FYPO:0002693 - resistance to diamide

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Genotypes:

FYPO:0009038 - resistance to egtazic acid

References:

Genotypes:

FYPO:0001453 - resistance to ethanol

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Genotypes:

FYPO:0001103 - resistance to hydrogen peroxide

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Genotypes:

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

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Genotypes:

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

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Genotypes:

FYPO:0002767 - resistance to terbinafine

References:

Genotypes:

FYPO:0000087 - sensitive to hydrogen peroxide

References:

Genotypes:

FYPO:0009086 - sensitive to lithium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0003656 - sensitive to vanadate

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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
PF00176SNF2-rel_domSNF2_NPfam
PF00271Helicase_CHelicase_C-likePfam
PF18585zf-CCCH_6Znf-CCCH_6Pfam
PF18586zf-CCCH_7Znf-CCCH_7Pfam
PF23615Chromo_MIT1Chromo_MIT1Pfam
cd15489PHD_SFCDD
cd17919DEXHc_SnfCDD
cd18793SF2_C_SNFSNF2/RAD54-like_CCDD
PS01359ZF_PHD_1Zinc_finger_PHD-type_CSPROSITE patterns
PS50016ZF_PHD_2Znf_PHD-fingerPROSITE profiles
PS51192HELICASE_ATP_BIND_1Helicase_ATP-bdPROSITE profiles
PS51194HELICASE_CTERHelicase_C-likePROSITE profiles
SM00249PHDZnf_PHDSMART
SM00487DEXDcHelicase_ATP-bdSMART
SM00490HELICcHelicase_C-likeSMART
G3DSA:3.40.50.10810:FF:000148CATH-FunFam
G3DSA:3.30.40.10Znf_RING/FYVE/PHDCATH-Gene3D
G3DSA:3.40.50.10810SNF2-like_sfCATH-Gene3D
G3DSA:3.40.50.300P-loop_NTPaseCATH-Gene3D
SSF52540P-loop_NTPaseSUPERFAMILY
SSF54160Chromo-like_dom_sfSUPERFAMILY
SSF57903Znf_FYVE_PHDSUPERFAMILY
PTHR45623PANTHER
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Low-complexitydisorder_predictionMobiDB-Low-complexity

Orthologs

References / Literature

PMID:23050226 - A genetic screen to discover pathways affecting cohesin function in Schizosaccharomyces pombe identifies chromatin effectors.
Chen Z et al. G3 (Bethesda) 2012 Oct;2(10):1161-8
PMID:27105116 - SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules.
Job G et al. Mol Cell 2016 Apr 21;62(2):207-221
PMID:22144463 - RNA elimination machinery targeting meiotic mRNAs promotes facultative heterochromatin formation.
Zofall M et al. Science 2012 Jan 06;335(6064):96-100
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:24013500 - A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism.
Marina DB et al. Genes Dev 2013 Sep 01;27(17):1851-6
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: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: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: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: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: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:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
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: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
GO_REF:0000002 - Comments
PMID:28228545 - Ablation of RNA interference and retrotransposons accompany acquisition and evolution of transposases to heterochromatin protein CENPB.
Upadhyay U et al. Mol Biol Cell 2017 Apr 15;28(8):1132-1146
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: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: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: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:21211723 - Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci.
Yamane K et al. Mol Cell 2011 Jan 07;41(1):56-66
PMID:23032292 - Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription.
Hennig BP et al. EMBO Rep 2012 Nov 06;13(11):997-1003
PMID:21333630 - Sde2: a novel nuclear protein essential for telomeric silencing and genomic stability in Schizosaccharomyces pombe.
Sugioka-Sugiyama R et al. Biochem Biophys Res Commun 2011 Mar 18;406(3):444-8
PMID:20118936 - Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.
Lantermann AB et al. Nat Struct Mol Biol 2010 Feb;17(2):251-7
PMID:31278118 - Cohesin Impedes Heterochromatin Assembly in Fission Yeast Cells Lacking Pds5.
Folco HD et al. Genetics 2019 Sep;213(1):127-141
PMID:30808655 - Transcriptional gene silencing requires dedicated interaction between HP1 protein Chp2 and chromatin remodeler Mit1.
Leopold K et al. Genes Dev 2019 May 01;33(9-10):565-577
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:32101745 - Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation.
Lee SY et al. Cell Rep 2020 Feb 25;30(8):2686-2698.e8
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:29167439 - Eroded telomeres are rearranged in quiescent fission yeast cells through duplications of subtelomeric sequences.
Maestroni L et al. Nat Commun 2017 Nov 22;8(1):1684
PMID:33378674 - The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin.
Shan CM et al. Cell Rep 2020 Dec 29;33(13):108561
PMID:17289569 - SHREC, an effector complex for heterochromatic transcriptional silencing.
Sugiyama T et al. Cell 2007 Feb 09;128(3):491-504
PMID:37400983 - Cooperative DNA-binding activities of Chp2 are critical for its function in heterochromatin assembly.
Rahayu AF et al. J Biochem 2023 Sep 29;174(4):371-382
PMID:38285941 - Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance.
Nathanailidou P et al. Proc Natl Acad Sci U S A 2024 Feb 06;121(6):e2315596121
PMID:32277274 - Conserved roles of chromatin remodellers in cohesin loading onto chromatin.
Muñoz S et al. Curr Genet 2020 Oct;66(5):951-956
PMID:39096900 - Nucleosome remodeler exclusion by histone deacetylation enforces heterochromatic silencing and epigenetic inheritance.
Sahu RK et al. Mol Cell 2024 Sep 05;84(17):3175-3191.e8
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:23103765 - CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.
Pointner J et al. EMBO J 2012 Nov 28;31(23):4388-403
PMID:39945308 - Characterization of the Swi6/HP1 binding motif in its partner protein reveals the basis for the functional divergence of the HP1 family proteins in fission yeast.
Oya T et al. FASEB J 2025 Feb 28;39(4):e70387
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: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:29618061 - Histone deacetylation promotes transcriptional silencing at facultative heterochromatin.
Watts BR et al. Nucleic Acids Res 2018 Jun 20;46(11):5426-5440
PMID:30110338 - The binding of Chp2's chromodomain to methylated H3K9 is essential for Chp2's role in heterochromatin assembly in fission yeast.
Maksimov V et al. PLoS One 2018;13(8):e0201101
PMID:19443688 - Diverse roles of HP1 proteins in heterochromatin assembly and functions in fission yeast.
Fischer T et al. Proc Natl Acad Sci U S A 2009 Jun 02;106(22):8998-9003
PMID:24662054 - The Mi-2 homolog Mit1 actively positions nucleosomes within heterochromatin to suppress transcription.
Creamer KM et al. Mol Cell Biol 2014 Jun;34(11):2046-61
PMID:33260998 - High-Throughput Flow Cytometry Combined with Genetic Analysis Brings New Insights into the Understanding of Chromatin Regulation of Cellular Quiescence.
Zahedi Y et al. Int J Mol Sci 2020 Nov 27;21(23)
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:19136623 - Phosphorylation of Swi6/HP1 regulates transcriptional gene silencing at heterochromatin.
Shimada A et al. Genes Dev 2009 Jan 01;23(1):18-23