H33_ARATH
ID H33_ARATH Reviewed; 136 AA.
AC P59169; Q6NR95;
DT 10-JAN-2003, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=Histone H3.3;
DE AltName: Full=Histone H3.2;
GN Name=HTR4; OrderedLocusNames=At4g40030; ORFNames=T5J17.200;
GN and
GN Name=HTR5; OrderedLocusNames=At4g40040; ORFNames=T5J17.210;
GN and
GN Name=HTR8; OrderedLocusNames=At5g10980; ORFNames=T30N20_250, T5K6.6;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=1593639; DOI=10.1016/0022-2836(92)90943-e;
RA Chaubet N., Clement B., Gigot C.;
RT "Genes encoding a histone H3.3-like variant in Arabidopsis contain
RT intervening sequences.";
RL J. Mol. Biol. 225:569-574(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Kim C.J., Chen H., Quinitio C., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP METHYLATION AT LYS-10.
RX PubMed=12456661; DOI=10.1093/emboj/cdf657;
RA Soppe W.J.J., Jasencakova Z., Houben A., Kakutani T., Meister A.,
RA Huang M.S., Jacobsen S.E., Schubert I., Fransz P.F.;
RT "DNA methylation controls histone H3 lysine 9 methylation and
RT heterochromatin assembly in Arabidopsis.";
RL EMBO J. 21:6549-6559(2002).
RN [9]
RP PHOSPHORYLATION AT SER-11 AND SER-29.
RX PubMed=14610360; DOI=10.1159/000074175;
RA Gernand D., Demidov D., Houben A.;
RT "The temporal and spatial pattern of histone H3 phosphorylation at serine
RT 28 and serine 10 is similar in plants but differs between mono- and
RT polycentric chromosomes.";
RL Cytogenet. Genome Res. 101:172-176(2003).
RN [10]
RP ACETYLATION AT LYS-10 AND LYS-19, AND METHYLATION AT LYS-5 AND LYS-10.
RX PubMed=12581305; DOI=10.1046/j.1365-313x.2003.01638.x;
RA Jasencakova Z., Soppe W.J.J., Meister A., Gernand D., Turner B.M.,
RA Schubert I.;
RT "Histone modifications in Arabidopsis -- high methylation of H3 lysine 9 is
RT dispensable for constitutive heterochromatin.";
RL Plant J. 33:471-480(2003).
RN [11]
RP DEVELOPMENTAL STAGE.
RX PubMed=15010610; DOI=10.1023/b:plan.0000019059.56489.ca;
RA Menges M., Hennig L., Gruissem W., Murray J.A.H.;
RT "Genome-wide gene expression in an Arabidopsis cell suspension.";
RL Plant Mol. Biol. 53:423-442(2003).
RN [12]
RP METHYLATION AT LYS-10.
RX PubMed=15014946; DOI=10.1007/s00412-004-0275-7;
RA Jackson J.P., Johnson L., Jasencakova Z., Zhang X., PerezBurgos L.,
RA Singh P.B., Cheng X., Schubert I., Jenuwein T., Jacobsen S.E.;
RT "Dimethylation of histone H3 lysine 9 is a critical mark for DNA
RT methylation and gene silencing in Arabidopsis thaliana.";
RL Chromosoma 112:308-315(2004).
RN [13]
RP INTERACTION WITH CMT3.
RX PubMed=15457214; DOI=10.1038/sj.emboj.7600430;
RA Lindroth A.M., Shultis D., Jasencakova Z., Fuchs J., Johnson L.,
RA Schubert D., Patnaik D., Pradhan S., Goodrich J., Schubert I., Jenuwein T.,
RA Khorasanizadeh S., Jacobsen S.E.;
RT "Dual histone H3 methylation marks at lysines 9 and 27 required for
RT interaction with CHROMOMETHYLASE3.";
RL EMBO J. 23:4286-4296(2004).
RN [14]
RP DEACETYLATION BY HDT1.
RX PubMed=14992728; DOI=10.1016/s1097-2765(04)00064-4;
RA Lawrence R.J., Earley K., Pontes O., Silva M., Chen Z.J., Neves N.,
RA Viegas W., Pikaard C.S.;
RT "A concerted DNA methylation/histone methylation switch regulates rRNA gene
RT dosage control and nucleolar dominance.";
RL Mol. Cell 13:599-609(2004).
RN [15]
RP ACETYLATION AT LYS-10; LYS-15; LYS-19 AND LYS-24, LACK OF ACETYLATION AT
RP LYS-28 AND LYS-37, METHYLATION AT LYS-5; LYS-10; LYS-19; LYS-24; LYS-28 AND
RP LYS-37, LACK OF METHYLATION AT LYS-15, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=15598823; DOI=10.1093/nar/gkh992;
RA Johnson L., Mollah S., Garcia B.A., Muratore T.L., Shabanowitz J.,
RA Hunt D.F., Jacobsen S.E.;
RT "Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct
RT combinations of post-translational modifications.";
RL Nucleic Acids Res. 32:6511-6518(2004).
RN [16]
RP METHYLATION AT LYS-5; LYS-10 AND LYS-28.
RX PubMed=14712277; DOI=10.1038/nature02269;
RA Bastow R., Mylne J.S., Lister C., Lippman Z., Martienssen R.A., Dean C.;
RT "Vernalization requires epigenetic silencing of FLC by histone
RT methylation.";
RL Nature 427:164-167(2004).
RN [17]
RP METHYLATION AT LYS-5.
RX PubMed=16258034; DOI=10.1105/tpc.105.034645;
RA Kim S.Y., He Y., Jacob Y., Noh Y.-S., Michaels S., Amasino R.;
RT "Establishment of the vernalization-responsive, winter-annual habit in
RT Arabidopsis requires a putative histone H3 methyl transferase.";
RL Plant Cell 17:3301-3310(2005).
RN [18]
RP METHYLATION AT LYS-37.
RX PubMed=16299497; DOI=10.1038/ncb1329;
RA Zhao Z., Yu Y., Meyer D., Wu C., Shen W.-H.;
RT "Prevention of early flowering by expression of FLOWERING LOCUS C requires
RT methylation of histone H3 K36.";
RL Nat. Cell Biol. 7:1256-1260(2005).
RN [19]
RP PHOSPHORYLATION AT SER-11; THR-12 AND SER-29.
RX PubMed=15753571; DOI=10.1159/000082394;
RA Houben A., Demidov D., Rutten T., Scheidtmann K.H.;
RT "Novel phosphorylation of histone H3 at threonine 11 that temporally
RT correlates with condensation of mitotic and meiotic chromosomes in plant
RT cells.";
RL Cytogenet. Genome Res. 109:148-155(2005).
RN [20]
RP IDENTIFICATION, DEVELOPMENTAL STAGE, AND TISSUE SPECIFICITY.
RX PubMed=16262706; DOI=10.1111/j.1365-313x.2005.02554.x;
RA Okada T., Endo M., Singh M.B., Bhalla P.L.;
RT "Analysis of the histone H3 gene family in Arabidopsis and identification
RT of the male-gamete-specific variant AtMGH3.";
RL Plant J. 44:557-568(2005).
RN [21]
RP ACETYLATION AT LYS-15 BY HAG1, AND DEACETYLATION BY HDA6.
RX PubMed=16648464; DOI=10.1101/gad.1417706;
RA Earley K., Lawrence R.J., Pontes O., Reuther R., Enciso A.J., Silva M.,
RA Neves N., Gross M., Viegas W., Pikaard C.S.;
RT "Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale
RT gene silencing in nucleolar dominance.";
RL Genes Dev. 20:1283-1293(2006).
RN [22]
RP REVIEW.
RX PubMed=16546438; DOI=10.1016/j.tplants.2006.02.008;
RA Fuchs J., Demidov D., Houben A., Schubert I.;
RT "Chromosomal histone modification patterns -- from conservation to
RT diversity.";
RL Trends Plant Sci. 11:199-208(2006).
RN [23]
RP ACETYLATION, AND METHYLATION AT LYS-28.
RX PubMed=17174094; DOI=10.1016/j.cub.2006.11.052;
RA Greb T., Mylne J.S., Crevillen P., Geraldo N., An H., Gendall A.R.,
RA Dean C.;
RT "The PHD finger protein VRN5 functions in the epigenetic silencing of
RT Arabidopsis FLC.";
RL Curr. Biol. 17:73-78(2007).
RN [24]
RP ACETYLATION AT LYS-15.
RX PubMed=17363895; DOI=10.1038/sj.emboj.7601647;
RA Wang X., Zhang Y., Ma Q., Zhang Z., Xue Y., Bao S., Chong K.;
RT "SKB1-mediated symmetric dimethylation of histone H4R3 controls flowering
RT time in Arabidopsis.";
RL EMBO J. 26:1934-1941(2007).
RN [25]
RP METHYLATION AT LYS-28, AND SUBCELLULAR LOCATION.
RX PubMed=17439305; DOI=10.1371/journal.pbio.0050129;
RA Zhang X., Clarenz O., Cokus S., Bernatavichute Y.V., Pellegrini M.,
RA Goodrich J., Jacobsen S.E.;
RT "Whole-genome analysis of histone H3 lysine 27 trimethylation in
RT Arabidopsis.";
RL PLoS Biol. 5:1026-1035(2007).
RN [26]
RP INTERACTION WITH AHL27.
RX PubMed=24218605; DOI=10.1073/pnas.1219277110;
RA Zhao J., Favero D.S., Peng H., Neff M.M.;
RT "Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by
RT interacting with each other via the PPC/DUF296 domain.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:E4688-E4697(2013).
RN [27]
RP INTERACTION WITH HIRA, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=25086063; DOI=10.1242/bio.20148680;
RA Nie X., Wang H., Li J., Holec S., Berger F.;
RT "The HIRA complex that deposits the histone H3.3 is conserved in
RT Arabidopsis and facilitates transcriptional dynamics.";
RL Biol. Open 3:794-802(2014).
RN [28]
RP MUTAGENESIS OF THR-32, AND METHYLATION AT LYS-28.
RX PubMed=24626927; DOI=10.1126/science.1248357;
RA Jacob Y., Bergamin E., Donoghue M.T., Mongeon V., LeBlanc C., Voigt P.,
RA Underwood C.J., Brunzelle J.S., Michaels S.D., Reinberg D., Couture J.F.,
RA Martienssen R.A.;
RT "Selective methylation of histone H3 variant H3.1 regulates heterochromatin
RT replication.";
RL Science 343:1249-1253(2014).
CC -!- FUNCTION: Variant histone H3 which replaces conventional H3 in a wide
CC range of nucleosomes in active genes. Constitutes the predominant form
CC of histone H3 in non-dividing cells and is incorporated into chromatin
CC independently of DNA synthesis. Deposited at sites of nucleosomal
CC displacement throughout transcribed genes, suggesting that it
CC represents an epigenetic imprint of transcriptionally active chromatin.
CC Nucleosomes wrap and compact DNA into chromatin, limiting DNA
CC accessibility to the cellular machineries which require DNA as a
CC template. Histones thereby play a central role in transcription
CC regulation, DNA repair, DNA replication and chromosomal stability. DNA
CC accessibility is regulated via a complex set of post-translational
CC modifications of histones, also called histone code, and nucleosome
CC remodeling.
CC -!- SUBUNIT: The nucleosome is a histone octamer containing two molecules
CC each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and
CC two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of
CC DNA. The H3K9meK27me dimethylated N-terminal tail of histone H3 can
CC directly interact with the chromodomains of CMT3 and/or LHP1. Interacts
CC with AHL27. Binds to HIRA (PubMed:25086063).
CC {ECO:0000269|PubMed:24218605, ECO:0000269|PubMed:25086063}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17439305,
CC ECO:0000269|PubMed:25086063}. Chromosome {ECO:0000269|PubMed:17439305}.
CC Nucleus, nucleolus {ECO:0000269|PubMed:25086063}. Note=Localized at
CC rDNA loci in the nucleolus. {ECO:0000269|PubMed:25086063}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=P59169-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:16262706}.
CC -!- DEVELOPMENTAL STAGE: Expressed in a replication-independent manner.
CC Strong expression in the generative cell of early bicellular pollen,
CC but not detected in late bicellular and tricellular pollen.
CC {ECO:0000269|PubMed:15010610, ECO:0000269|PubMed:16262706}.
CC -!- PTM: Can be acetylated to form H3K9ac, H3K14ac, H3K18ac and H3K23ac.
CC H3K9ac could compete with H3K9me and prevent gene silencing.
CC H3K9acK14ac molecules are 30-fold less abundant than H3K9ac or H3K14ac.
CC Very low level of H3K9meK14ac. H3K14 is specifically acetylated by HAG1
CC and deacetylated by HDA6. H3K9ac is deacetylated by HDT1. H3K9ac is
CC restricted to euchromatin. H3K18ac, but not H3K9ac, is cell-cycle
CC dependent and linked to replication. Reduced H4R3me2s increases H3K14ac
CC in the FLC chromatin and activates or maintains its transcription.
CC Vernalization decreases H3K9/14ac in the promoter region of FLC.
CC {ECO:0000269|PubMed:12581305, ECO:0000269|PubMed:15598823,
CC ECO:0000269|PubMed:16648464, ECO:0000269|PubMed:17174094,
CC ECO:0000269|PubMed:17363895}.
CC -!- PTM: Mono-, di- or trimethylated to form mainly H3K4me1/2/3,
CC H3K9me1/2/3 and H3K36me1/2/3. Very low monomethylation at H3K18me1 or
CC H3K23me1. H3K4me1/2/3, H3K9me3, H3K27me3 and H3K36me1/2/3 are typical
CC marks for euchromatin, whereas heterochromatic chromocenters are
CC enriched in H3K9me1/2 and H3K27me1/2. H3K27me3 is largely restricted to
CC the transcribed regions of single genes and not associated with low-
CC nucleosome density regions. SUVR1 to SUVR5, ASHH1 to ASHH3 and ASHR1 to
CC ASHR3 methylate H3, with ASHH2 methylating specifically H3K4 and H3K36.
CC Monomethylation at H3K27me1 by ATXR5/6 is inhibited by the presence of
CC Thr-32. The Su(var)3-9 homolog proteins (SUVH1 to SUVH10) are H3K9-
CC specific methyltransferases. Among them, KRYPTONITE (SUVH4) is only
CC involved in di- or trimethylation. Regarding H3K9, the major forms are
CC H3K9me1 (20%) and H3K9me2 (10%), while H3K9me3 is rare (0.2%). H3K9me
CC is controlled by DNA methylation and is not required for the formation
CC of constitutive heterochromatin, but double methylation H3K9meK27me is
CC required for the recruitment of CMT3 to methylate heterochromatin and
CC silence euchromatic loci. Very low level of H3K9meK14ac. 36% of H3K27
CC is found under the form of H3K27me1 and 6% of H3K27me2, with no
CC detectable H3K27me3. 6% of H3K36 is found under the form of H3K36me1,
CC 15% of H3K36me2 and 3% of H3K36me3. H3K27me2K36me1 is found in 15% of
CC the proteins while H3k27me1K36me2 is not detected. H2BK143ub1 is
CC probably prerequisite for H3K4me. Elevated H3K4me3 and H3K36me2 formed
CC by ASHH2 are required for high FLC expression. Vernalization increases
CC H3K9me2 and H3K27me2/3 and decreases H3K4me2 at the FLC locus,
CC resulting in the epigenetic silencing of this floral repressor.
CC {ECO:0000269|PubMed:12456661, ECO:0000269|PubMed:12581305,
CC ECO:0000269|PubMed:14712277, ECO:0000269|PubMed:15014946,
CC ECO:0000269|PubMed:15598823, ECO:0000269|PubMed:16258034,
CC ECO:0000269|PubMed:16299497, ECO:0000269|PubMed:17174094,
CC ECO:0000269|PubMed:17439305, ECO:0000269|PubMed:24626927}.
CC -!- PTM: In meta- and anaphase, H3T11ph is found on the entire length of
CC the condensed chromosomes, whereas H3S10ph and H3S28ph are confined to
CC the pericentromeric regions. During the first meiotic division, H3S10ph
CC and H3S28ph are found on the entire length of the chromosome. Both
CC sites may be involved in sister chromatid cohesion. No phosphorylation
CC detected during interphase. AUR1 and AUR2 phosphorylate only H3S10,
CC while AUR3 phosphorylates both H3S10 and H3S28.
CC {ECO:0000269|PubMed:14610360, ECO:0000269|PubMed:15753571}.
CC -!- SIMILARITY: Belongs to the histone H3 family. {ECO:0000305}.
CC -!- CAUTION: To ensure consistency between histone entries, we follow the
CC 'Brno' nomenclature for histone modifications, with positions referring
CC to those used in the literature for the 'closest' model organism. Due
CC to slight variations in histone sequences between organisms and to the
CC presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the
CC actual positions of modified amino acids in the sequence generally
CC differ. In this entry the following conventions are used: H3K4me1/2/3 =
CC mono-, di- and trimethylated Lys-5; H3K9me1/2/3 = mono-, di- and
CC trimethylated Lys-10; H3K9ac = acetylated Lys-10; H3S10ph =
CC phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac =
CC acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 =
CC monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 =
CC monomethylated Lys-24; H3K27me1/2/3 = mono-, di- and trimethylated Lys-
CC 28; H3S28ph = phosphorylated Ser-29; H3K36me1/2/3 = mono-, di- and
CC trimethylated Lys-37. {ECO:0000305}.
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DR EMBL; X60429; CAA42958.1; -; Genomic_DNA.
DR EMBL; X60429; CAA42957.1; -; Genomic_DNA.
DR EMBL; AL161596; CAB80666.1; -; Genomic_DNA.
DR EMBL; AL161596; CAB80667.1; -; Genomic_DNA.
DR EMBL; AL035708; CAB38916.1; -; Genomic_DNA.
DR EMBL; AL035708; CAB38917.1; -; Genomic_DNA.
DR EMBL; AL365234; CAB96853.1; -; Genomic_DNA.
DR EMBL; AL391222; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002687; AEE87155.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE87157.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE87158.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE87159.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66215.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM67333.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91617.1; -; Genomic_DNA.
DR EMBL; AF385735; AAK60325.1; -; mRNA.
DR EMBL; AY078027; AAL77728.1; -; mRNA.
DR EMBL; AY070749; AAL50088.1; -; mRNA.
DR EMBL; AY097375; AAM19891.1; -; mRNA.
DR EMBL; BT002391; AAO00751.1; -; mRNA.
DR EMBL; BT003326; AAO29945.1; -; mRNA.
DR EMBL; AY086668; AAM63725.1; -; mRNA.
DR EMBL; BT025499; ABF58917.1; -; mRNA.
DR PIR; S24346; S24346.
DR RefSeq; NP_001031816.1; NM_001036739.1. [P59169-1]
DR RefSeq; NP_001078517.1; NM_001085048.2. [P59169-1]
DR RefSeq; NP_001328124.1; NM_001342564.1. [P59169-1]
DR RefSeq; NP_001329167.1; NM_001342565.1. [P59169-1]
DR RefSeq; NP_195713.1; NM_120167.4. [P59169-1]
DR RefSeq; NP_196659.1; NM_121136.6. [P59169-1]
DR RefSeq; NP_849529.1; NM_179198.2. [P59169-1]
DR PDB; 4PL6; X-ray; 1.68 A; C/D=2-12.
DR PDB; 4PLI; X-ray; 1.65 A; C/D=33-42.
DR PDB; 4PLL; X-ray; 2.60 A; C/D=33-42.
DR PDBsum; 4PL6; -.
DR PDBsum; 4PLI; -.
DR PDBsum; 4PLL; -.
DR AlphaFoldDB; P59169; -.
DR SMR; P59169; -.
DR BioGRID; 15444; 17.
DR BioGRID; 15445; 12.
DR BioGRID; 16243; 10.
DR STRING; 3702.AT4G40030.2; -.
DR iPTMnet; P59169; -.
DR PaxDb; P59169; -.
DR EnsemblPlants; AT4G40030.1; AT4G40030.1; AT4G40030. [P59169-1]
DR EnsemblPlants; AT4G40030.3; AT4G40030.3; AT4G40030. [P59169-1]
DR EnsemblPlants; AT4G40030.4; AT4G40030.4; AT4G40030. [P59169-1]
DR EnsemblPlants; AT4G40040.1; AT4G40040.1; AT4G40040. [P59169-1]
DR EnsemblPlants; AT4G40040.2; AT4G40040.2; AT4G40040. [P59169-1]
DR EnsemblPlants; AT4G40040.3; AT4G40040.3; AT4G40040. [P59169-1]
DR EnsemblPlants; AT5G10980.1; AT5G10980.1; AT5G10980. [P59169-1]
DR GeneID; 830164; -.
DR GeneID; 830165; -.
DR GeneID; 830965; -.
DR Gramene; AT4G40030.1; AT4G40030.1; AT4G40030. [P59169-1]
DR Gramene; AT4G40030.3; AT4G40030.3; AT4G40030. [P59169-1]
DR Gramene; AT4G40030.4; AT4G40030.4; AT4G40030. [P59169-1]
DR Gramene; AT4G40040.1; AT4G40040.1; AT4G40040. [P59169-1]
DR Gramene; AT4G40040.2; AT4G40040.2; AT4G40040. [P59169-1]
DR Gramene; AT4G40040.3; AT4G40040.3; AT4G40040. [P59169-1]
DR Gramene; AT5G10980.1; AT5G10980.1; AT5G10980. [P59169-1]
DR KEGG; ath:AT4G40030; -.
DR KEGG; ath:AT4G40040; -.
DR KEGG; ath:AT5G10980; -.
DR Araport; AT4G40030; -.
DR Araport; AT4G40040; -.
DR Araport; AT5G10980; -.
DR TAIR; locus:2140025; AT4G40040.
DR TAIR; locus:2183795; AT5G10980.
DR eggNOG; KOG1745; Eukaryota.
DR HOGENOM; CLU_078295_4_0_1; -.
DR InParanoid; P59169; -.
DR OMA; HIVMART; -.
DR PhylomeDB; P59169; -.
DR PRO; PR:P59169; -.
DR Proteomes; UP000006548; Chromosome 4.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; P59169; baseline and differential.
DR Genevisible; P59169; AT.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0030875; C:rDNA protrusion; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046982; F:protein heterodimerization activity; IEA:InterPro.
DR GO; GO:0030527; F:structural constituent of chromatin; IEA:InterPro.
DR Gene3D; 1.10.20.10; -; 1.
DR InterPro; IPR009072; Histone-fold.
DR InterPro; IPR007125; Histone_H2A/H2B/H3.
DR InterPro; IPR000164; Histone_H3/CENP-A.
DR PANTHER; PTHR11426; PTHR11426; 1.
DR Pfam; PF00125; Histone; 1.
DR PRINTS; PR00622; HISTONEH3.
DR SMART; SM00428; H3; 1.
DR SUPFAM; SSF47113; SSF47113; 1.
DR PROSITE; PS00322; HISTONE_H3_1; 1.
DR PROSITE; PS00959; HISTONE_H3_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Chromosome; DNA-binding;
KW Methylation; Nucleosome core; Nucleus; Phosphoprotein; Reference proteome.
FT CHAIN 1..136
FT /note="Histone H3.3"
FT /id="PRO_0000221268"
FT REGION 1..43
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 15
FT /note="Not N6-methylated"
FT /evidence="ECO:0000269|PubMed:15598823"
FT SITE 28
FT /note="Not N6-acetylated"
FT /evidence="ECO:0000269|PubMed:15598823"
FT SITE 32
FT /note="Impaired recognition by ATXR5 and ATXR6"
FT /evidence="ECO:0000269|PubMed:24626927"
FT SITE 37
FT /note="Not N6-acetylated"
FT /evidence="ECO:0000269|PubMed:15598823"
FT MOD_RES 5
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:12581305,
FT ECO:0000269|PubMed:14712277, ECO:0000269|PubMed:15598823,
FT ECO:0000269|PubMed:16258034"
FT MOD_RES 5
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:12581305,
FT ECO:0000269|PubMed:14712277, ECO:0000269|PubMed:15598823,
FT ECO:0000269|PubMed:16258034"
FT MOD_RES 5
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:12581305,
FT ECO:0000269|PubMed:14712277, ECO:0000269|PubMed:15598823,
FT ECO:0000269|PubMed:16258034"
FT MOD_RES 10
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:12456661,
FT ECO:0000269|PubMed:12581305, ECO:0000269|PubMed:14712277,
FT ECO:0000269|PubMed:15014946, ECO:0000269|PubMed:15598823"
FT MOD_RES 10
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:12456661,
FT ECO:0000269|PubMed:12581305, ECO:0000269|PubMed:14712277,
FT ECO:0000269|PubMed:15014946, ECO:0000269|PubMed:15598823"
FT MOD_RES 10
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:12581305,
FT ECO:0000269|PubMed:15598823"
FT MOD_RES 10
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:12456661,
FT ECO:0000269|PubMed:12581305, ECO:0000269|PubMed:14712277,
FT ECO:0000269|PubMed:15014946, ECO:0000269|PubMed:15598823"
FT MOD_RES 11
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:14610360,
FT ECO:0000269|PubMed:15753571"
FT MOD_RES 12
FT /note="Phosphothreonine"
FT /evidence="ECO:0000269|PubMed:15753571"
FT MOD_RES 15
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:15598823,
FT ECO:0000269|PubMed:16648464, ECO:0000269|PubMed:17363895"
FT MOD_RES 19
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:12581305,
FT ECO:0000269|PubMed:15598823"
FT MOD_RES 19
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:15598823"
FT MOD_RES 24
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:15598823"
FT MOD_RES 24
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:15598823"
FT MOD_RES 28
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P59226"
FT MOD_RES 28
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:14712277,
FT ECO:0000269|PubMed:15598823, ECO:0000269|PubMed:17174094,
FT ECO:0000269|PubMed:17439305, ECO:0000269|PubMed:24626927"
FT MOD_RES 28
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:14712277,
FT ECO:0000269|PubMed:15598823, ECO:0000269|PubMed:17174094,
FT ECO:0000269|PubMed:17439305, ECO:0000269|PubMed:24626927"
FT MOD_RES 29
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:14610360,
FT ECO:0000269|PubMed:15753571"
FT MOD_RES 37
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:15598823,
FT ECO:0000269|PubMed:16299497"
FT MOD_RES 37
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:15598823,
FT ECO:0000269|PubMed:16299497"
FT MOD_RES 37
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000269|PubMed:15598823,
FT ECO:0000269|PubMed:16299497"
FT MUTAGEN 32
FT /note="T->A: H3K27me1 methylation by ATXR5/6 restored."
FT /evidence="ECO:0000269|PubMed:24626927"
SQ SEQUENCE 136 AA; 15406 MW; 6D72383BF2E9EBE6 CRC64;
MARTKQTARK STGGKAPRKQ LATKAARKSA PTTGGVKKPH RYRPGTVALR EIRKYQKSTE
LLIRKLPFQR LVREIAQDFK TDLRFQSHAV LALQEAAEAY LVGLFEDTNL CAIHAKRVTI
MPKDIQLARR IRGERA
