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protein coding gene - spt6 (SPAC1F7.01c) - histone H3-H4 chaperone Spt6

Gene summary

Standard name
spt6
Systematic ID
SPAC1F7.01c
Product
histone H3-H4 chaperone Spt6
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
SPAC694.07c
UniProt ID
Q09915
ORFeome ID
30/30F06
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 4212476..4216861 reverse strand

Annotation

Comment

PBO:0011110 - Spt6 binding correlates with that of RNAPII at the heterochromatin

References:

GO biological process

GO:0006366 - transcription by RNA polymerase II

References:

GO:0140673 - transcription elongation-coupled chromatin remodeling

References:

GO cellular component

GO:0005634 - nucleus

References:

GO:0005721 - pericentric heterochromatin

References:

GO:0008023 - transcription elongation factor complex

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GO molecular function

GO:0003677 - DNA binding

References:

GO:0000511 - H2A-H2B histone complex chaperone activity

References:

GO:0000510 - H3-H4 histone complex chaperone activity

References:

GO:0042393 - histone binding

References:

GO:0031491 - nucleosome binding

References:

GO:0005515 - protein binding

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Modification

MOD:00046 - O-phospho-L-serine

References:

MOD:00047 - O-phospho-L-threonine

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MOD:00696 - phosphorylated residue

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MOD:01148 - ubiquitinylated lysine

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Multi-locus phenotype

FYPO:0006403 - abolished histone H3-K36 dimethylation at promoter during vegetative growth

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0005048 - increased protein localization to chromatin at RNA polymerase II promoter during vegetative growth

References:

Genotypes:

FYPO:0001387 - loss of viability at high temperature

References:

Genotypes:

FYPO:0007347 - normal histone H3-K36 trimethylation during vegetative growth

References:

Genotypes:

FYPO:0003241 - unequal mitotic sister chromatid segregation

References:

Genotypes:

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0000886 - abnormal histone H3-K9 dimethylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0000864 - abnormal histone H3-K9 trimethylation at centromere during vegetative growth

References:

Genotypes:

FYPO:0000865 - abnormal histone H3-K9 trimethylation at centromere inner repeat during vegetative growth

References:

Genotypes:

FYPO:0000885 - abnormal histone H3-K9 trimethylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0000854 - abnormal nucleosome positioning in euchromatin

References:

Genotypes:

FYPO:0000855 - abnormal nucleosome positioning in heterochromatin

References:

Genotypes:

FYPO:0002919 - abolished histone H3-K36 methylation during vegetative growth

References:

Genotypes:

FYPO:0002917 - abolished histone H3-K4 methylation during vegetative growth

References:

Genotypes:

FYPO:0000082 - decreased cell population growth at high temperature

References:

Genotypes:

FYPO:0000080 - decreased cell population growth at low temperature

References:

Genotypes:

FYPO:0003743 - decreased cell population growth during glucose starvation

References:

Genotypes:

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

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Genotypes:

FYPO:0000684 - decreased cell population growth on glycerol carbon source

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Genotypes:

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

References:

Genotypes:

FYPO:0002834 - decreased chromatin silencing at centromere

References:

Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

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Genotypes:

FYPO:0003216 - decreased chromatin silencing at rDNA

References:

Genotypes:

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

References:

Genotypes:

FYPO:0004604 - decreased chromatin silencing at subtelomere

References:

Genotypes:

FYPO:0002367 - decreased histone H3-K4 dimethylation during vegetative growth

References:

Genotypes:

FYPO:0002368 - decreased histone H3-K4 trimethylation during vegetative growth

References:

Genotypes:

FYPO:0000888 - decreased histone H3-K9 dimethylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0000708 - decreased mating efficiency

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Genotypes:

FYPO:0000470 - decreased mating type switching

References:

Genotypes:

FYPO:0004313 - decreased protein localization to CENP-A containing chromatin

References:

Genotypes:

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

References:

Genotypes:

FYPO:0002910 - decreased protein localization to chromatin at transcribed regions during vegetative growth

References:

Genotypes:

FYPO:0001117 - decreased RNA level during vegetative growth

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0002906 - increased antisense primary transcript splicing

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Genotypes:

FYPO:0002913 - increased antisense RNA transcription

References:

Genotypes:

FYPO:0005258 - increased cell population growth at high temperature

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

References:

Genotypes:

FYPO:0009072 - increased cell population growth on lysine nitrogen source

References:

Genotypes:

FYPO:0009098 - increased cell population growth on mannitol carbon source

References:

Genotypes:

FYPO:0000220 - increased centromeric outer repeat transcript level

References:

Genotypes:

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

References:

Genotypes:

FYPO:0002369 - increased histone H3-K56 acetylation at centromere outer repeat during vegetative growth

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Genotypes:

FYPO:0002370 - increased histone H3-K56 acetylation in transcribed regions during vegetative growth

References:

Genotypes:

FYPO:0000893 - increased histone H3-K9 acetylation at centromere during vegetative growth

References:

Genotypes:

FYPO:0006814 - increased histone H3-K9 acetylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0000879 - increased histone H3-K9 trimethylation during vegetative growth

References:

Genotypes:

FYPO:0007310 - increased histone H4-K12 acetylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0007311 - increased histone H4-K16 acetylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0007309 - increased histone H4-K8 acetylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0002914 - increased intergenic transcription

References:

Genotypes:

FYPO:0000786 - increased plasmid loss

References:

Genotypes:

FYPO:0000825 - increased RNA level during vegetative growth

References:

Genotypes:

FYPO:0004557 - increased vegetative cell population growth

References:

Genotypes:

FYPO:0000245 - loss of viability in stationary phase

References:

Genotypes:

FYPO:0002923 - normal histone H2B-K119 ubiquitination during vegetative growth

References:

Genotypes:

FYPO:0000862 - normal histone H3-K9 dimethylation at centromere during vegetative growth

References:

Genotypes:

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

References:

Genotypes:

FYPO:0000857 - normal nucleosome positioning in euchromatin

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Genotypes:

FYPO:0000858 - normal nucleosome positioning in heterochromatin

References:

Genotypes:

FYPO:0000067 - resistance to brefeldin A

References:

Genotypes:

FYPO:0000073 - resistance to caffeine

References:

Genotypes:

FYPO:0009068 - resistance to ciclopirox olamine

References:

Genotypes:

FYPO:0000764 - resistance to cycloheximide

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Genotypes:

FYPO:0009038 - resistance to egtazic acid

References:

Genotypes:

FYPO:0001453 - resistance to ethanol

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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:0009070 - resistance to itraconazole

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Genotypes:

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

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Genotypes:

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

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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:0002767 - resistance to terbinafine

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Genotypes:

FYPO:0003383 - resistance to tert-butyl hydroperoxide

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Genotypes:

FYPO:0007808 - resistance to valproic acid

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Genotypes:

FYPO:0000830 - resistance to vanadate

References:

Genotypes:

FYPO:0009065 - resistance to X-rays and rapamycin during vegetative growth

References:

Genotypes:

FYPO:0009062 - resistance to X-rays during vegetative growth

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Genotypes:

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

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Genotypes:

FYPO:0001701 - sensitive to bortezomib

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Genotypes:

FYPO:0000096 - sensitive to cadmium

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Genotypes:

FYPO:0000097 - sensitive to caffeine during vegetative growth

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Genotypes:

FYPO:0009080 - sensitive to calcofluor and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0001188 - sensitive to Calcofluor White

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Genotypes:

FYPO:0003840 - sensitive to carbendazim

References:

Genotypes:

FYPO:0000104 - sensitive to cycloheximide

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Genotypes:

FYPO:0000799 - sensitive to diamide

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Genotypes:

FYPO:0007931 - sensitive to egtazic acid

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Genotypes:

FYPO:0000785 - sensitive to formamide

References:

Genotypes:

FYPO:0000087 - sensitive to hydrogen peroxide

References:

Genotypes:

FYPO:0001719 - sensitive to lithium

References:

Genotypes:

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

References:

Genotypes:

FYPO:0006836 - sensitive to magnesium chloride

References:

Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

References:

Genotypes:

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

References:

Genotypes:

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

References:

Genotypes:

FYPO:0000841 - sensitive to sodium dodecyl sulfate

References:

Genotypes:

FYPO:0000091 - sensitive to thiabendazole

References:

Genotypes:

FYPO:0002701 - sensitive to torin1

References:

Genotypes:

FYPO:0001457 - sensitive to tunicamycin

References:

Genotypes:

FYPO:0000115 - sensitive to valproic acid

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

PBO:0006222 - predominantly single copy (one to one)

Protein features

IDNameInterPro nameDB name
PF14632SPT6_acidicSpt6_acidic_N_domPfam
PF14633SH2_2Spt6_SH2Pfam
PF14635HHH_7Spt6_HHHPfam
PF14639YqgFSpt6_YqgFPfam
PF14641HTH_44Spt6_HTH_DNA-bd_domPfam
PF21710Spt6_S1Spt6-like_S1Pfam
PF22706Tex_central_regionTex-like_central_regionPfam
cd00164S1_likeCDD
cd09918SH2_Nterm_SPT6_likeSpt6_SH2_NCDD
cd09928SH2_Cterm_SPT6_likeSpt6_SH2_CCDD
PS50126S1S1_domainPROSITE profiles
SM00316S1S1_domainSMART
SM00732YqgFcYqgF/RNaseH-like_domSMART
G3DSA:1.10.10.2740:FF:000002CATH-FunFam
G3DSA:1.10.150.850:FF:000001CATH-FunFam
G3DSA:3.30.505.10:FF:000056CATH-FunFam
G3DSA:3.30.505.10:FF:000065CATH-FunFam
G3DSA:1.10.10.2740Spt6_death-likeCATH-Gene3D
G3DSA:1.10.10.650Tex-like_HTH_dom_sfCATH-Gene3D
G3DSA:1.10.150.850CATH-Gene3D
G3DSA:1.10.3500.10Tex-like_dom_sfCATH-Gene3D
G3DSA:2.40.50.140NA-bd_OB-foldCATH-Gene3D
G3DSA:3.30.420.140YqgF/RNaseH-like_dom_sfCATH-Gene3D
G3DSA:3.30.505.10SH2_dom_sfCATH-Gene3D
SSF158832SUPERFAMILY
SSF47781RuvA_2-likeSUPERFAMILY
SSF50249NA-bd_OB-foldSUPERFAMILY
SSF53098RNaseH-like_sfSUPERFAMILY
SSF55550SH2_dom_sfSUPERFAMILY
PTHR10145TF_Spt6PANTHER
PIRSF036947Spt6TF_Spt6PIRSF
CoilCOILS
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Low-complexitydisorder_predictionMobiDB-Low-complexity
mobidb-lite-Negative-Polyelectrolytedisorder_predictionMobiDB-Negative-Polyelectrolyte
mobidb-lite-Polardisorder_predictionMobiDB-Polar

Orthologs

References / Literature

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: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
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:23950735 - Global analysis of fission yeast mating genes reveals new autophagy factors.
Sun LL et al. PLoS Genet 2013;9(8):e1003715
PMID:21844224 - Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe.
Kiely CM et al. Mol Cell Biol 2011 Oct;31(20):4193-204
PMID:28218250 - Chromatin remodeller Fun30 Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation.
Lee J et al. Nat Commun 2017 Feb 20;8:14527
GO_REF:0000002 - Comments
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: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:40737126 - The histone core domain evolves at single-residue resolution to directly orchestrate transcription.
Harvey ZH et al. Cell Rep 2025 Aug 26;44(8):116079
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:25375137 - Systematic analysis of the role of RNA-binding proteins in the regulation of RNA stability.
Hasan A et al. PLoS Genet 2014 Nov;10(11):e1004684
PMID:29852001 - New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe.
Maki T et al. PLoS Genet 2018 May;14(5):e1007424
PMID:30793188 - A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation.
Gopalakrishnan R et al. Nucleic Acids Res 2019 May 07;47(8):3888-3903
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:33468217 - Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex.
Weigt M et al. Epigenetics Chromatin 2021 Jan 19;14(1):8
PMID:15507118 - An interactive gene network for securin-separase, condensin, cohesin, Dis1/Mtc1 and histones constructed by mass transformation.
Yuasa T et al. Genes Cells 2004 Nov;9(11):1069-82
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: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:23028377 - Factors that promote H3 chromatin integrity during transcription prevent promiscuous deposition of CENP-A(Cnp1) in fission yeast.
Choi ES et al. PLoS Genet 2012 Sep;8(9):e1002985
PMID:23851719 - Spt6 prevents transcription-coupled loss of posttranslationally modified histone H3.
Kato H et al. Sci Rep 2013;3:2186
PMID:21712547 - Mitotic substrates of the kinase aurora with roles in chromatin regulation identified through quantitative phosphoproteomics of fission yeast.
Koch A et al. Sci Signal 2011 Jun 28;4(179):rs6
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:29967244 - Histone Chaperone Asf1 Is Required for the Establishment of Repressive Chromatin in Schizosaccharomyces pombe fbp1 Gene Repression.
Umeda M et al. Mol Cell Biol 2018 Sep 15;38(18)
PMID:24107707 - Spt6: two fundamentally distinct functions in the regulation of histone modification.
Kato H et al. Epigenetics 2013 Dec;8(12):1249-53
PMID:35970865 - The Mis6 inner kinetochore subcomplex maintains CENP-A nucleosomes against centromeric non-coding transcription during mitosis.
Hirai H et al. Commun Biol 2022 Aug 15;5(1):818
PMID:28974540 - The fission yeast nucleoporin Alm1 is required for proteasomal degradation of kinetochore components.
Salas-Pino S et al. J Cell Biol 2017 Nov 06;216(11):3591-3608
PMID:37052630 - Tfs1, transcription elongation factor TFIIS, has an impact on chromosome segregation affected by pka1 deletion in Schizosaccharomyces pombe.
Takenaka K et al. Curr Genet 2023 Jun;69(2-3):115-125
PMID:40972526 - The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain.
Warner JL et al. Mol Cell 2025 Sep 18;85(18):3407-3424.e8
PMID:18257517 - Phosphoproteome analysis of fission yeast.
Wilson-Grady JT et al. J Proteome Res 2008 Mar;7(3):1088-97
PMID:24210919 - Mtr4-like protein coordinates nuclear RNA processing for heterochromatin assembly and for telomere maintenance.
Lee NN et al. Cell 2013 Nov 21;155(5):1061-74
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: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: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:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.
Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
PMID:24100010 - Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast.
DeGennaro CM et al. Mol Cell Biol 2013 Dec;33(24):4779-92
PMID:26098123 - Promoter nucleosome dynamics regulated by signalling through the CTD code.
Materne P et al. Elife 2015 Jun 22;4:e09008
PMID:28366642 - Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation.
Shetty A et al. Mol Cell 2017 Apr 06;66(1):77-88.e5
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:27298342 - Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks.
Willis NA et al. Proc Natl Acad Sci U S A 2016 Jun 28;113(26):E3676-85