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protein coding gene - hhf3 (SPBC1105.12) - histone H4 h4.3

Gene summary

Standard name
hhf3
Systematic ID
SPBC1105.12
Product
histone H4 h4.3
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
h4.3
UniProt ID
P09322
ORFeome ID
39/39G04
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 3529767..3530388 forward strand

Annotation

Disease association

MONDO:0030729 - Tessadori-van Haaften neurodevelopmental syndrome 1

References:

MONDO:0030730 - Tessadori-van Haaften neurodevelopmental syndrome 2

References:

MONDO:0030993 - Tessadori-Van Haaften neurodevelopmental syndrome 3

References:

MONDO:0031000 - Tessadori-Van Haaften neurodevelopmental syndrome 4

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GO biological process

GO:0006338 - chromatin remodeling

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GO cellular component

GO:0000786 - nucleosome

References:

GO:0005634 - nucleus

References:

GO molecular function

GO:0140463 - chromatin-protein adaptor activity

References:

GO:0005515 - protein binding

References:

GO:0030527 - structural constituent of chromatin

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Modification

MOD:00427 - methylated residue

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MOD:00394 - monoacetylated residue

References:

MOD:00083 - N6,N6,N6-trimethyl-L-lysine

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MOD:00084 - N6,N6-dimethyl-L-lysine

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MOD:00085 - N6-methyl-L-lysine

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MOD:01148 - ubiquitinylated lysine

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Multi-locus phenotype

FYPO:0005341 - decreased chromatin binding during cellular response to hydroxyurea

References:

Genotypes:

FYPO:0005951 - decreased nucleosome occupancy at highly transcribed RNA polymerase II genes

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Genotypes:

FYPO:0005948 - decreased protein localization to chromatin at highly transcribed RNA polymerase II genes during vegetative growth

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Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

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Genotypes:

FYPO:0006413 - increased level of histone gene mRNA during vegetative growth

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

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Genotypes:

FYPO:0001164 - normal growth on glucose carbon source

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Genotypes:

FYPO:0000963 - normal growth on hydroxyurea

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Genotypes:

FYPO:0005952 - normal nucleosome occupancy at highly transcribed RNA polymerase II genes

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Genotypes:

FYPO:0001357 - normal vegetative cell population growth

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Genotypes:

Protein features

PBO:0111763 - histone fold

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PomGeneEx:0000012 - RNA level decreased

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PomGeneEx:0000017 - RNA level fluctuates

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PomGeneEx:0000011 - RNA level increased

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Quantitative gene expression

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0005011 - decreased histone H4 acetylation during vegetative growth

References:

Genotypes:

FYPO:0007324 - decreased level of histone H4 in cell

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Genotypes:

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

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Genotypes:

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

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Genotypes:

FYPO:0006518 - loss of viability in G0

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Genotypes:

FYPO:0007553 - normal G1 to G0 transition

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Genotypes:

FYPO:0009038 - resistance to egtazic acid

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Genotypes:

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

References:

Genotypes:

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

References:

Genotypes:

FYPO:0003383 - resistance to tert-butyl hydroperoxide

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Genotypes:

FYPO:0000830 - resistance to vanadate

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Genotypes:

FYPO:0000085 - sensitive to camptothecin

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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

Protein features

IDNameInterPro nameDB name
PF15511CENP-T_CCENP-T/H4_CPfam
cd22912HFD_H4Histone_H4CDD
PS00047HISTONE_H4Histone_H4_CSPROSITE patterns
SM00417H4Histone_H4SMART
PR00623HISTONEH4Histone_H4PRINTS
G3DSA:1.10.20.10:FF:000007CATH-FunFam
G3DSA:1.10.20.10Histone-foldCATH-Gene3D
SSF47113Histone-foldSUPERFAMILY
PTHR10484Histone_H4PANTHER

Orthologs

References / Literature

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: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
PMID:27901072 - Characterisation of functional domains in fission yeast Ams2 that are required for core histone gene transcription.
Takayama Y et al. Sci Rep 2016 Nov 30;6:38111
PMID:17190600 - Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair.
Botuyan MV et al. Cell 2006 Dec 29;127(7):1361-73
PMID:12535531 - A cell cycle-regulated GATA factor promotes centromeric localization of CENP-A in fission yeast.
Chen ES et al. Mol Cell 2003 Jan;11(1):175-87
PMID:26896847 - Ensembl comparative genomics resources.
Herrero J et al. Database (Oxford) 2016;2016
GO_REF:0000050 - Manual transfer of GO annotation data to genes by curator judgment of sequence model
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
GO_REF:0000051 - S. pombe keyword mapping
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:38376141 - Disordered regions and folded modules in CAF-1 promote histone deposition in Schizosaccharomyces pombe .
Ouasti F et al. Elife 2024 Feb 20;12
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:39094570 - A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance.
Yu J et al. Cell 2024 Sep 05;187(18):5010-5028.e24
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
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
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:29804820 - Mis16 Switches Function from a Histone H4 Chaperone to a CENP-A Cnp1 -Specific Assembly Factor through Eic1 Interaction.
An S et al. Structure 2018 Jul 03;26(7):960-971.e4
PMID:30321377 - Proteomic profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome.
Telekawa C et al. Nucleic Acids Res 2018 Nov 30;46(21):11169-11183
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:30992049 - The NuA4 acetyltransferase and histone H4 acetylation promote replication recovery after topoisomerase I-poisoning.
Noguchi C et al. Epigenetics Chromatin 2019 Apr 16;12(1):24
PMID:16537923 - Sterol regulatory element binding protein is a principal regulator of anaerobic gene expression in fission yeast.
Todd BL et al. Mol Cell Biol 2006 Apr;26(7):2817-31
PMID:18579787 - The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module.
Stuwe T et al. Proc Natl Acad Sci U S A 2008 Jul 01;105(26):8884-9
PMID:22540037 - Predicting the fission yeast protein interaction network.
Pancaldi V et al. G3 (Bethesda) 2012 Apr;2(4):453-67
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:26412298 - A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival.
Beckley JR et al. Mol Cell Proteomics 2015 Dec;14(12):3132-41
PMID:39705284 - Proteomic and phosphoproteomic analyses reveal that TORC1 is reactivated by pheromone signaling during sexual reproduction in fission yeast.
Bérard M et al. PLoS Biol 2024 Dec 20;22(12):e3002963
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:22771823 - Schizosaccharomyces pombe Hat1 (Kat1) is associated with Mis16 and is required for telomeric silencing.
Tong K et al. Eukaryot Cell 2012 Sep;11(9):1095-103
PMID:22150589 - Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA.
Qiu Y et al. Biochem J 2012 Mar 15;442(3):527-38
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
PB_REF:0000001 - Protein modification annotation by manual transfer of experimentally-verified annotation data to orthologs based on curator judgment of sequence features.
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
PMID:33670267 - The Role of Non-Catalytic Domains of Hrp3 in Nucleosome Remodeling.
Dong W et al. Int J Mol Sci 2021 Feb 11;22(4)
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:20230746 - Hsk1- and SCF(Pof3)-dependent proteolysis of S. pombe Ams2 ensures histone homeostasis and centromere function.
Takayama Y et al. Dev Cell 2010 Mar 16;18(3):385-96
PMID:39878217 - The ortholog of human DNAJC9 promotes histone H3-H4 degradation and is counteracted by Asf1 in fission yeast.
Ding Y et al. Nucleic Acids Res 2025 Jan 24;53(3)
PMID:31371524 - Subunit interactions and arrangements in the fission yeast Mis16-Mis18-Mis19 complex.
Korntner-Vetter M et al. Life Sci Alliance 2019 Aug;2(4)
PMID:20403971 - Proteomic and functional analysis of the noncanonical poly(A) polymerase Cid14.
Keller C et al. RNA 2010 Jun;16(6):1124-9
PMID:24478943 - Pcf1, a large subunit of CAF-1, required for maintenance of checkpoint kinase Cds1 activity.
Kunoh T et al. Springerplus 2014;3:30
PMID:30503616 - Centromere DNA Destabilizes H3 Nucleosomes to Promote CENP-A Deposition during the Cell Cycle.
Shukla M et al. Curr Biol 2018 Dec 17;28(24):3924-3936.e4
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:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.
Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
PMID:25002536 - A novel histone deacetylase complex in the control of transcription and genome stability.
Zilio N et al. Mol Cell Biol 2014 Sep 15;34(18):3500-14
PMID:15897182 - Two distinct pathways responsible for the loading of CENP-A to centromeres in the fission yeast cell cycle.
Takahashi K et al. Philos Trans R Soc Lond B Biol Sci 2005 Mar 29;360(1455):595-606; discussion 606-7