Reviewed, UniProtKB/Swiss-Prot P84243 (H33_HUMAN)

Names and origin

Protein names

Recommended name:
    Histone H3.3

Gene names

Name:	H3F3A
Synonyms:	H3.3A, H3F3
ORF Names:	PP781
AND
Name:	H3F3B
Synonyms:	H3.3B

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	136 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
Subunit structure	The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Interacts with HIRA, a chaperone required for its incorporation into nucleosomes.
Subcellular location	Nucleus.
Developmental stage	Expressed throughout the cell cycle independently of DNA synthesis.
Post-translational modification	Acetylation is generally linked to gene activation. Acetylation on Lys-10 impairs methylation at Arg-9. Acetylation on Lys-19 and Lys-24 favors methylation at Arg-18. Citrullination at Arg-9 and/or Arg-18 by PADI4 impairs methylation and represses transcription. Asymmetric dimethylation at Arg-18 by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 by PRMT5 is linked to gene repression. Specifically enriched in modifications associated with active chromatin such as methylation at Lys-5, Lys-37 and Lys-80. Methylation at Lys-5 facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 and Lys-28, which are linked to gene repression, are underrepresented. Methylation at Lys-10 is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 and acetylation of H3 and H4. Methylation at Lys-5 and Lys-80 require preliminary monoubiquitination of H2B at 'Lys-120'. Methylation at Lys-10 and Lys-28 are enriched in inactive X chromosome chromatin. Phosphorylated at Thr-4 by GSG2/haspin during prophase and dephosphorylated during anaphase. At centromeres, specifically phosphorylated at Thr-12 from prophase to early anaphase, probably DAPK3. Phosphorylation at 'Ser-11' by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at 'Ser-11' by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11, which is linked to gene activation, prevents methylation at Lys-10 but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at 'Ser-11' is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 by MLTK isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation on Ser-32 is specific to regions bordering centromeres in metaphase chromosomes. Ubiquitinated By similarity.
Sequence similarities	Belongs to the histone H3 family.
Sequence caution	The sequence CAH73371.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Cellular component	Chromosomal protein Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Citrullination Methylation Phosphoprotein Ubl conjugation
Technical term	Direct protein sequencing
Gene Ontology (GO)
Biological process	nucleosome assembly Inferred from electronic annotation. Source: InterPro
Cellular component	nucleosome Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed
	Chain	2 – 136	135	Histone H3.3		PRO_0000221247
Amino acid modifications
	Modified residue	4	1	Phosphothreonine
	Modified residue	5	1	N6-acetyllysine; alternate
	Modified residue	5	1	N6-methyllysine; alternate
	Modified residue	9	1	Citrulline; alternate
	Modified residue	9	1	Symmetric dimethylarginine; by PRMT5; alternate By similarity
	Modified residue	10	1	N6,N6,N6-trimethyllysine; alternate
	Modified residue	10	1	N6,N6-dimethyllysine; alternate
	Modified residue	10	1	N6-acetyllysine; alternate
	Modified residue	10	1	N6-methyllysine; alternate
	Modified residue	11	1	Phosphoserine
	Modified residue	12	1	Phosphothreonine
	Modified residue	15	1	N6-acetyllysine
	Modified residue	18	1	Asymmetric dimethylarginine; by CARM1; alternate
	Modified residue	18	1	Citrulline; alternate
	Modified residue	19	1	N6-acetyllysine; alternate
	Modified residue	19	1	N6-methyllysine; alternate
	Modified residue	24	1	N6-acetyllysine; alternate
	Modified residue	24	1	N6-methyllysine; alternate
	Modified residue	28	1	N6,N6,N6-trimethyllysine; alternate
	Modified residue	28	1	N6,N6-dimethyllysine; alternate
	Modified residue	28	1	N6-acetyllysine; alternate
	Modified residue	28	1	N6-methyllysine; alternate
	Modified residue	29	1	Phosphoserine
	Modified residue	32	1	Phosphoserine
	Modified residue	37	1	N6,N6,N6-trimethyllysine; alternate
	Modified residue	37	1	N6,N6-dimethyllysine; alternate
	Modified residue	37	1	N6-acetyllysine; alternate
	Modified residue	37	1	N6-methyllysine; alternate
	Modified residue	57	1	N6,N6,N6-trimethyllysine; alternate
	Modified residue	57	1	N6-acetyllysine; alternate
	Modified residue	57	1	N6-methyllysine; alternate
	Modified residue	65	1	N6-methyllysine
	Modified residue	80	1	N6,N6,N6-trimethyllysine; alternate Probable
	Modified residue	80	1	N6,N6-dimethyllysine; alternate
	Modified residue	80	1	N6-acetyllysine; alternate
	Modified residue	80	1	N6-methyllysine; alternate
	Modified residue	123	1	N6-methyllysine
Experimental info
	Sequence conflict	9	1	R → L in AAH81561. Ref.7

Sequences

	Sequence		Length	Mass (Da)
	P84243-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 5158ED279E6F9E1C	FASTA	136	15,328
	10 20 30 40 50 60 MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE 70 80 90 100 110 120 LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI 130 MPKDIQLARR IRGERA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure of a human histone cDNA: evidence that basally expressed histone genes have intervening sequences and encode polyadenylylated mRNAs." Wells D., Kedes L. Proc. Natl. Acad. Sci. U.S.A. 82:2834-2838(1985) [PubMed: 2859593] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (H3F3A). Tissue: Fibroblast.
[2]	"Unusual structure, evolutionary conservation of non-coding sequences and numerous pseudogenes characterize the human H3.3 histone multigene family." Wells D., Hoffman D., Kedes L. Nucleic Acids Res. 15:2871-2889(1987) [PubMed: 3031613] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (H3F3A).
[3]	"The human replacement histone H3.3B gene (H3F3B)." Albig W., Bramlage B., Gruber K., Klobeck H.-G., Kunz J., Doenecke D. Genomics 30:264-272(1995) [PubMed: 8586426] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3F3B). Tissue: Testis.
[4]	"Large-scale cDNA transfection screening for genes related to cancer development and progression." Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X. , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J. Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed: 15498874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]	The German cDNA consortium Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (H3F3B). Tissue: Retina.
[6]	"The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R. Nature 441:315-321(2006) [PubMed: 16710414] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (H3F3A AND H3F3B). Tissue: Bone marrow, Brain, Colon, Eye, Lung, Muscle, Spinal cord, Testis and Uterus.
[8]	"Human spleen histone H3. Isolation and amino acid sequence." Ohe Y., Iwai K. J. Biochem. 90:1205-1211(1981) [PubMed: 7309716] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, METHYLATION AT LYS-10; LYS-28 AND LYS-37, ACETYLATION AT LYS-15 AND LYS-24.
[9]	"Modifications of human histone H3 variants during mitosis." Garcia B.A., Barber C.M., Hake S.B., Ptak C., Turner F.B., Busby S.A., Shabanowitz J., Moran R.G., Allis C.D., Hunt D.F. Biochemistry 44:13202-13213(2005) [PubMed: 16185088] [Abstract] Cited for: PROTEIN SEQUENCE OF 28-41, METHYLATION AT LYS-5; LYS-10; LYS-28 AND LYS-37, PHOSPHORYLATION AT THR-4; SER-11; SER-29 AND SER-32, ACETYLATION AT LYS-10 AND LYS-15, MASS SPECTROMETRY.
[10]	"Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation." Goto H., Tomono Y., Ajiro K., Kosako H., Fujita M., Sakurai M., Okawa K., Iwamatsu A., Okigaki T., Takahashi T., Inagaki M. J. Biol. Chem. 274:25543-25549(1999) [PubMed: 10464286] [Abstract] Cited for: PROTEIN SEQUENCE OF 58-64; 117-120 AND 124-135, PHOSPHORYLATION AT SER-11 AND SER-29.
[11]	"Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins." Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Nature 410:116-120(2001) [PubMed: 11242053] [Abstract] Cited for: METHYLATION AT LYS-10.
[12]	"Aurora-B phosphorylates Histone H3 at serine28 with regard to the mitotic chromosome condensation." Goto H., Yasui Y., Nigg E.A., Inagaki M. Genes Cells 7:11-17(2002) [PubMed: 11856369] [Abstract] Cited for: PHOSPHORYLATION AT SER-11 AND SER-29.
[13]	"Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase." Preuss U., Landsberg G., Scheidtmann K.H. Nucleic Acids Res. 31:878-885(2003) [PubMed: 12560483] [Abstract] Cited for: PHOSPHORYLATION AT SER-11 AND THR-12.
[14]	"Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis." Tagami H., Ray-Gallet D., Almouzni G., Nakatani Y. Cell 116:51-61(2004) [PubMed: 14718166] [Abstract] Cited for: FUNCTION, INTERACTION WITH HIRA.
[15]	"Ligand-dependent activation of the farnesoid X-receptor directs arginine methylation of histone H3 by CARM1." Ananthanarayanan M., Li S., Balasubramaniyan N., Suchy F.J., Walsh M.J. J. Biol. Chem. 279:54348-54357(2004) [PubMed: 15471871] [Abstract] Cited for: METHYLATION AT ARG-18.
[16]	"Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks." Huyen Y., Zgheib O., Ditullio R.A. Jr., Gorgoulis V.G., Zacharatos P., Petty T.J., Sheston E.A., Mellert H.S., Stavridi E.S., Halazonetis T.D. Nature 432:406-411(2004) [PubMed: 15525939] [Abstract] Cited for: METHYLATION AT LYS-80.
[17]	"Human PAD4 regulates histone arginine methylation levels via demethylimination." Wang Y., Wysocka J., Sayegh J., Lee Y.-H., Perlin J.R., Leonelli L., Sonbuchner L.S., McDonald C.H., Cook R.G., Dou Y., Roeder R.G., Clarke S., Stallcup M.R., Allis C.D., Coonrod S.A. Science 306:279-283(2004) [PubMed: 15345777] [Abstract] Cited for: CITRULLINATION AT ARG-9 AND ARG-18, METHYLATION AT ARG-18.
[18]	"Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division." Chow C.-M., Georgiou A., Szutorisz H., Maia e Silva A., Pombo A., Barahona I., Dargelos E., Canzonetta C., Dillon N. EMBO Rep. 6:354-360(2005) [PubMed: 15776021] [Abstract] Cited for: FUNCTION.
[19]	"The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment." Dai J., Sultan S., Taylor S.S., Higgins J.M.G. Genes Dev. 19:472-488(2005) [PubMed: 15681610] [Abstract] Cited for: PHOSPHORYLATION AT THR-4; SER-11 AND SER-29.
[20]	"Phosphorylation of Ser28 in histone H3 mediated by mixed lineage kinase-like mitogen-activated protein triple kinase alpha." Choi H.S., Choi B.Y., Cho Y.-Y., Zhu F., Bode A.M., Dong Z. J. Biol. Chem. 280:13545-13553(2005) [PubMed: 15684425] [Abstract] Cited for: PHOSPHORYLATION AT SER-29.
[21]	"Serine 31 phosphorylation of histone variant H3.3 is specific to regions bordering centromeres in metaphase chromosomes." Hake S.B., Garcia B.A., Kauer M., Baker S.P., Shabanowitz J., Hunt D.F., Allis C.D. Proc. Natl. Acad. Sci. U.S.A. 102:6344-6349(2005) [PubMed: 15851689] [Abstract] Cited for: PHOSPHORYLATION AT SER-11; SER-29 AND SER-32, MASS SPECTROMETRY.
[22]	"Histone H3.3 deposition at E2F-regulated genes is linked to transcription." Daury L., Chailleux C., Bonvallet J., Trouche D. EMBO Rep. 7:66-71(2006) [PubMed: 16258499] [Abstract] Cited for: FUNCTION.
[23]	"Expression patterns and post-translational modifications associated with mammalian histone H3 variants." Hake S.B., Garcia B.A., Duncan E.M., Kauer M., Dellaire G., Shabanowitz J., Bazett-Jones D.P., Allis C.D., Hunt D.F. J. Biol. Chem. 281:559-568(2006) [PubMed: 16267050] [Abstract] Cited for: ACETYLATION AT LYS-10; LYS-15; LYS-19; LYS-24 AND LYS-28, METHYLATION AT LYS-5; LYS-10; LYS-19; LYS-28; LYS-37; LYS-65; LYS-80 AND LYS-123, MASS SPECTROMETRY.
[24]	"Mass spectrometric characterization of human histone H3: a bird's eye view." Thomas C.E., Kelleher N.L., Mizzen C.A. J. Proteome Res. 5:240-247(2006) [PubMed: 16457588] [Abstract] Cited for: METHYLATION AT LYS-5 AND LYS-10, ACETYLATION AT LYS-10, MASS SPECTROMETRY.
[25]	"Substrate and functional diversity of lysine acetylation revealed by a proteomics survey." Kim S.C., Sprung R., Chen Y., Xu Y., Ball H., Pei J., Cheng T., Kho Y., Xiao H., Xiao L., Grishin N.V., White M., Yang X.-J., Zhao Y. Mol. Cell 23:607-618(2006) [PubMed: 16916647] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-10; LYS-15; LYS-19; LYS-24; LYS-28 AND LYS-37, MASS SPECTROMETRY. Tissue: Epithelium.
[26]	"Coactivator-associated arginine methyltransferase-1 enhances nuclear factor-kappaB-mediated gene transcription through methylation of histone H3 at arginine 17." Miao F., Li S., Chavez V., Lanting L., Natarajan R. Mol. Endocrinol. 20:1562-1573(2006) [PubMed: 16497732] [Abstract] Cited for: ACETYLATION AT LYS-10 AND LYS-15, METHYLATION AT ARG-18, CITRULLINATION AT ARG-18.
[27]	"Organismal differences in post-translational modifications in histones H3 and H4." Garcia B.A., Hake S.B., Diaz R.L., Kauer M., Morris S.A., Recht J., Shabanowitz J., Mishra N., Strahl B.D., Allis C.D., Hunt D.F. J. Biol. Chem. 282:7641-7655(2007) [PubMed: 17194708] [Abstract] Cited for: ACETYLATION AT LYS-5; LYS-10; LYS-15; LYS-19; LYS-24; LYS-28; LYS-37; LYS-57 AND LYS-80, METHYLATION AT LYS-5; LYS-10; LYS-19; LYS-24; LYS-28; LYS-37; LYS-57; LYS-65; LYS-80 AND LYS-123, MASS SPECTROMETRY.
[28]	"Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification." Morris S.A., Rao B., Garcia B.A., Hake S.B., Diaz R.L., Shabanowitz J., Hunt D.F., Allis C.D., Lieb J.D., Strahl B.D. J. Biol. Chem. 282:7632-7640(2007) [PubMed: 17189264] [Abstract] Cited for: ACETYLATION AT LYS-37.
[29]	"Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra." Yu L.-R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D. J. Proteome Res. 6:4150-4162(2007) [PubMed: 17924679] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-29, MASS SPECTROMETRY. Tissue: Epithelium.
+	Additional computationally mapped references.

Web resources

Wikipedia

Histone H3 entry

Cross-references

Sequence databases
EMBLGenBankDDBJ	M11354 mRNA. Translation: AAA52653.1. M11353 mRNA. Translation: AAA52654.1. Z48950 Genomic DNA. Translation: CAA88778.1