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protein coding gene - pht1 (SPBC11B10.10c) - histone H2A variant H2A.Z Pht1

Gene summary

Standard name
pht1
Systematic ID
SPBC11B10.10c
Product
histone H2A variant H2A.Z Pht1
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
pi001
UniProt ID
P48003
ORFeome ID
41/41D01
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 1502203..1503444 reverse strand

Annotation

GO biological process

GO:0140898 - CENP-A eviction from euchromatin

References:

GO:0006325 - chromatin organization

References:

GO:0006338 - chromatin remodeling

References:

GO:0031507 - heterochromatin formation

References:

GO cellular component

GO:0000785 - chromatin

References:

GO:0000791 - euchromatin

References:

GO:0000786 - nucleosome

References:

GO:0005634 - nucleus

References:

GO molecular function

GO:0003677 - DNA binding

References:

GO:0030527 - structural constituent of chromatin

References:

Multi-locus phenotype

FYPO:0001946 - abolished mitotic sister chromatid separation

References:

Genotypes:

FYPO:0003217 - decreased chromatin silencing at centromere central core

References:

Genotypes:

FYPO:0003029 - decreased mRNA splicing, via spliceosome

References:

Genotypes:

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

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0005887 - ectopic CENP-A containing chromatin assembly

References:

Genotypes:

FYPO:0003557 - increased antisense RNA level

References:

Genotypes:

FYPO:0001489 - inviable vegetative cell

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0000228 - lagging mitotic chromosomes

References:

Genotypes:

FYPO:0003619 - normal mRNA splicing, via spliceosome

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0000095 - sensitive to bleomycin

References:

Genotypes:

FYPO:0000091 - sensitive to thiabendazole

References:

Genotypes:

Protein features

PBO:0111763 - histone fold

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0000427 - abnormal G1 to G0 transition

References:

Genotypes:

FYPO:0000121 - abnormal sporulation

References:

Genotypes:

FYPO:0003556 - abnormal transcription termination

References:

Genotypes:

FYPO:0000227 - chromosome loss during mitotic chromosome segregation

References:

Genotypes:

FYPO:0009100 - decreased cell population growth on glycerol and galactose carbon source

References:

Genotypes:

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

References:

Genotypes:

FYPO:0006686 - decreased DNA double-strand break processing

References:

Genotypes:

FYPO:0004516 - decreased number of Rad52 foci during vegetative growth

References:

Genotypes:

FYPO:0007710 - decreased number of Ssb1 foci

References:

Genotypes:

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

References:

Genotypes:

FYPO:0007199 - decreased splicing of mRNA introns with nonconsensus cis-splicing sequences

References:

Genotypes:

FYPO:0005318 - decreased transcription from MCB promoter

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0009007 - decreased vegetative cell population viability

References:

Genotypes:

FYPO:0009012 - decreased vegetative cell population viability on galactose carbon source

References:

Genotypes:

FYPO:0005887 - ectopic CENP-A containing chromatin assembly

References:

Genotypes:

FYPO:0006372 - incomplete meiotic chromosome segregation, with chromosomal bridge

References:

Genotypes:

FYPO:0003557 - increased antisense RNA level

References:

Genotypes:

FYPO:0003938 - increased cell population growth during glucose starvation

References:

Genotypes:

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

References:

Genotypes:

FYPO:0005261 - increased cell population growth on galactose carbon source

References:

Genotypes:

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

References:

Genotypes:

FYPO:0009094 - increased cell population growth on lysine and proline nitrogen source

References:

Genotypes:

FYPO:0009096 - increased cell population growth on xylose carbon source

References:

Genotypes:

FYPO:0002664 - increased level of stress responsive gene mRNA during vegetative growth

References:

Genotypes:

FYPO:0004342 - increased LTR-derived RNA level

References:

Genotypes:

FYPO:0001840 - increased minichromosome loss during vegetative growth

References:

Genotypes:

FYPO:0006741 - increased nucleosome occupancy at MCB promoters

References:

Genotypes:

FYPO:0001908 - increased pre-mRNA level

References:

Genotypes:

FYPO:0003105 - increased transposable element-derived small RNA level

References:

Genotypes:

FYPO:0004557 - increased vegetative cell population growth

References:

Genotypes:

FYPO:0009008 - increased vegetative cell population viability

References:

Genotypes:

FYPO:0001309 - increased viability in stationary phase

References:

Genotypes:

FYPO:0004163 - increased viability upon glucose starvation

References:

Genotypes:

FYPO:0004343 - increased wtf-derived RNA level

References:

Genotypes:

FYPO:0001404 - irregular colony morphology

References:

Genotypes:

FYPO:0006518 - loss of viability in G0

References:

Genotypes:

FYPO:0000245 - loss of viability in stationary phase

References:

Genotypes:

FYPO:0005231 - loss of viability in stationary phase upon glucose starvation

References:

Genotypes:

FYPO:0000283 - mitotic chromosome fragmentation upon segregation

References:

Genotypes:

FYPO:0002360 - normal chromatin silencing at centromere

References:

Genotypes:

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

References:

Genotypes:

FYPO:0003555 - normal chromatin silencing at subtelomere

References:

Genotypes:

FYPO:0001383 - normal DNA content

References:

Genotypes:

FYPO:0007328 - normal number of Rad52 foci during vegetative growth

References:

Genotypes:

FYPO:0007711 - normal number of Ssb1 foci

References:

Genotypes:

FYPO:0006742 - normal transcription from MCB promoter

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0000067 - resistance to brefeldin A

References:

Genotypes:

FYPO:0009079 - resistance to calcofluor and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0001029 - resistance to canavanine

References:

Genotypes:

FYPO:0002693 - resistance to diamide

References:

Genotypes:

FYPO:0009047 - resistance to dimethyl sulfoxide

References:

Genotypes:

FYPO:0009038 - resistance to egtazic acid

References:

Genotypes:

FYPO:0001453 - resistance to ethanol

References:

Genotypes:

FYPO:0009034 - resistance to ethylenediaminetetraacetic acid

References:

Genotypes:

FYPO:0002047 - resistance to heat shock during nitrogen starvation

References:

Genotypes:

FYPO:0001583 - resistance to lithium

References:

Genotypes:

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

References:

Genotypes:

FYPO:0000725 - resistance to methyl methanesulfonate

References:

Genotypes:

FYPO:0009039 - resistance to potassium chloride

References:

Genotypes:

FYPO:0000077 - resistance to rapamycin

References:

Genotypes:

FYPO:0005266 - resistance to sodium dodecyl sulfate

References:

Genotypes:

FYPO:0003383 - resistance to tert-butyl hydroperoxide

References:

Genotypes:

FYPO:0007933 - sensitive to 2,2′-dipyridyl

References:

Genotypes:

FYPO:0004325 - sensitive to 5-fluorouracil

References:

Genotypes:

FYPO:0009067 - sensitive to amorolfine

References:

Genotypes:

FYPO:0000440 - sensitive to antimycin A

References:

Genotypes:

FYPO:0000095 - sensitive to bleomycin

References:

Genotypes:

FYPO:0000096 - sensitive to cadmium

References:

Genotypes:

FYPO:0000097 - sensitive to caffeine during vegetative growth

References:

Genotypes:

FYPO:0007926 - sensitive to calcofluor and potassium chloride

References:

Genotypes:

FYPO:0000104 - sensitive to cycloheximide

References:

Genotypes:

FYPO:0000799 - sensitive to diamide

References:

Genotypes:

FYPO:0007931 - sensitive to egtazic acid

References:

Genotypes:

FYPO:0000842 - sensitive to ethanol during vegetative growth

References:

Genotypes:

FYPO:0000785 - sensitive to formamide

References:

Genotypes:

FYPO:0000087 - sensitive to hydrogen peroxide

References:

Genotypes:

FYPO:0000088 - sensitive to hydroxyurea

References:

Genotypes:

FYPO:0001719 - sensitive to lithium

References:

Genotypes:

FYPO:0009084 - sensitive to lithium chloride and methyl methanesulfonate

References:

Genotypes:

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

References:

Genotypes:

FYPO:0009088 - sensitive to magnesium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

References:

Genotypes:

FYPO:0007930 - sensitive to phloxine B and hydrogen peroxide

References:

Genotypes:

FYPO:0001214 - sensitive to potassium chloride

References:

Genotypes:

FYPO:0009082 - sensitive to potassium chloride and methyl methanesulfonate

References:

Genotypes:

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

References:

Genotypes:

FYPO:0002617 - sensitive to sodium butyrate

References:

Genotypes:

FYPO:0007925 - sensitive to sodium chloride and methyl methanesulfonate

References:

Genotypes:

FYPO:0009090 - sensitive to sodium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0000841 - sensitive to sodium dodecyl sulfate

References:

Genotypes:

FYPO:0000112 - sensitive to sorbitol

References:

Genotypes:

FYPO:0000086 - sensitive to tacrolimus

References:

Genotypes:

FYPO:0000797 - sensitive to tert-butyl hydroperoxide

References:

Genotypes:

FYPO:0000091 - sensitive to thiabendazole

References:

Genotypes:

FYPO:0002701 - sensitive to torin1

References:

Genotypes:

FYPO:0002546 - sensitive to trichostatin A

References:

Genotypes:

FYPO:0001457 - sensitive to tunicamycin

References:

Genotypes:

FYPO:0000268 - sensitive to UV during vegetative growth

References:

Genotypes:

FYPO:0000115 - sensitive to valproic acid

References:

Genotypes:

FYPO:0003656 - sensitive to vanadate

References:

Genotypes:

FYPO:0009064 - sensitive to X-rays and rapamycin during vegetative growth.

References:

Genotypes:

FYPO:0001234 - slow vegetative cell population growth

References:

Genotypes:

FYPO:0002405 - viable curved stubby vegetative cell

References:

Genotypes:

FYPO:0002112 - viable curved vegetative cell

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

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

Warnings

PBO:0000070 - gene structure updated

References:

PBO:0091725 - this gene was called cdc2L (cdc2 left) in PMID:16453669, name not added as potentially misleading

Protein features

IDNameInterPro nameDB name
PF16211Histone_H2A_CHistone_H2A_CPFAM
PF00125HistoneH2A/H2B/H3PFAM
cd00074HFD_H2AHistone_H2ACDD
PS00046HISTONE_H2AHistone_H2A_CSPROSITE_PATTERNS
SM00414h2a4Histone_H2ASMART
PR00620HISTONEH2AHistone_H2APRINTS
G3DSA:1.10.20.10:FF:000021FUNFAM
SSF47113Histone-foldHistone-foldSUPERFAMILY
G3DSA:1.10.20.10Histone, subunit AHistone-foldGENE3D
PTHR23430HISTONE H2AHistone_H2APANTHER
mobidb-lite-Disorderdisorder_predictionMOBIDB-Disorder
mobidb-lite-Positive-Polyelectrolytedisorder_predictionMOBIDB-Positive-Polyelectrolyte

Orthologs

References / Literature

PMID:27666591 - Ccp1 Homodimer Mediates Chromatin Integrity by Antagonizing CENP-A Loading.
Dong Q et al. Mol Cell 2016 Oct 06;64(1):79-91
PMID:21436456 - Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA.
Zhang K et al. Science 2011 Mar 25;331(6024):1624-7
PMID:28446597 - The histone variant H2A.Z promotes splicing of weak introns.
Nissen KE et al. Genes Dev 2017 Apr 01;31(7):688-701
PMID:21633354 - Condensin association with histone H2A shapes mitotic chromosomes.
Tada K et al. Nature 2011 Jun 01;474(7352):477-83
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:19160458 - Improved tools for efficient mapping of fission yeast genes: identification of microtubule nucleation modifier mod22-1 as an allele of chromatin- remodelling factor gene swr1.
Anders A et al. Yeast 2008 Dec;25(12):913-25
PMID:24013502 - Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries.
Wang J et al. Genes Dev 2013 Sep 01;27(17):1886-902
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: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:23173672 - Identification of novel genes involved in DNA damage response by screening a genome-wide Schizosaccharomyces pombe deletion library.
Pan X et al. BMC Genomics 2012 Nov 23;13:662
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
GO_REF:0000033 - Annotation inferences using phylogenetic trees
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: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:24687850 - H2A.Z-dependent regulation of cohesin dynamics on chromosome arms.
Tapia-Alveal C et al. Mol Cell Biol 2014 Jun;34(11):2092-104
PMID:23861937 - Genome-wide screening for genes associated with valproic acid sensitivity in fission yeast.
Zhang L et al. PLoS One 2013;8(7):e68738
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: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:17452352 - Differential regulation of repeated histone genes during the fission yeast cell cycle.
Takayama Y et al. Nucleic Acids Res 2007;35(10):3223-37
PMID:21901086 - Podbat: a novel genomic tool reveals Swr1-independent H2A.Z incorporation at gene coding sequences through epigenetic meta-analysis.
Sadeghi L et al. PLoS Comput Biol 2011 Aug;7(8):e1002163
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:27172183 - Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast.
Larson A et al. G3 (Bethesda) 2016 Jun 01;6(6):1513-23
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:40015273 - A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.
Skribbe M et al. Mol Cell 2025 Feb 19;
PMID:7808414 - Analysis of a histone H2A variant from fission yeast: evidence for a role in chromosome stability.
Carr AM et al. Mol Gen Genet 1994 Dec 01;245(5):628-35
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: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: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: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: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:25483073 - Chromosome segregation and organization are targets of 5'-Fluorouracil in eukaryotic cells.
Mojardín L et al. Cell Cycle 2015;14(2):206-18
PMID:21850271 - Genome-wide screening for genes associated with FK506 sensitivity in fission yeast.
Ma Y et al. PLoS One 2011;6(8):e23422
PMID:19547744 - Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
Beltrao P et al. PLoS Biol 2009 Jun 16;7(6):e1000134
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: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:16453669 - Transcription of the cdc2 cell cycle control gene of the fission yeast Schizosaccharomyces pombe.
Durkacz B et al. EMBO J 1986 Feb;5(2):369-73
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:28281664 - Genetic interactions and functional analyses of the fission yeast gsk3 and amk2 single and double mutants defective in TORC1-dependent processes.
Rallis C et al. Sci Rep 2017 Mar 10;7:44257
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:24634168 - Proteome-wide search for PP2A substrates in fission yeast.
Bernal M et al. Proteomics 2014 Jun;14(11):1367-80
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:29259000 - Genes Important for Schizosaccharomyces pombe Meiosis Identified Through a Functional Genomics Screen.
Blyth J et al. Genetics 2018 Feb;208(2):589-603
PMID:30134042 - The INO80 complex activates the transcription of S-phase genes in a cell cycle-regulated manner.
Knezevic I et al. FEBS J 2018 Oct;285(20):3870-3881
GO_REF:0000050 - Manual transfer of GO annotation data to genes by curator judgment of sequence model
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:28904333 - The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3.
Choi ES et al. Nat Commun 2017 Sep 13;8(1):529
PMID:33723569 - Schizosaccharomyces pombe KAT5 contributes to resection and repair of a DNA double-strand break.
Li T et al. Genetics 2021 May 17;218(1)
PMID:34496258 - Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription.
Heo DH et al. Cell Rep 2021 Sep 07;36(10):109671
PMID:19714215 - The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
Aligianni S et al. PLoS Genet 2009 Aug;5(8):e1000626
PMID:34984977 - Functional profiling of long intergenic non-coding RNAs in fission yeast.
Rodriguez-Lopez M et al. Elife 2022 Jan 05;11
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
PMID:37615341 - Schizosaccharomyces pombe Rtf2 is important for replication fork barrier activity of RTS1 via splicing of Rtf1 .
Budden AM et al. Elife 2023 Aug 24;12
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