ID   MBD9_ARATH              Reviewed;        2176 AA.
AC   Q9SGH2; Q9SSA6;
DT   08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   02-SEP-2026, entry version 170.
DE   RecName: Full=Methyl-CpG-binding domain-containing protein 9;
DE            Short=AtMBD9;
DE            Short=MBD09;
DE            EC=2.3.1.48;
DE   AltName: Full=Histone acetyl transferase MBD9;
DE   AltName: Full=Methyl-CpG-binding protein MBD9;
GN   Name=MBD9; OrderedLocusNames=At3g01460; ORFNames=F4P13.1, T13O15.10;
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 [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130713; DOI=10.1038/35048706;
RA   Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA   Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA   Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA   Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA   Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA   Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA   Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA   Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA   Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA   Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA   Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA   Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA   de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA   Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA   Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA   Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA   Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA   Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA   Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA   Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA   Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA   Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA   Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA   Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT   "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL   Nature 408:820-822(2000).
RN   [2]
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   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Resource (TAIR);
RT   "Community-consensus reference genome of Arabidopsis thaliana Col-0.";
RL   Submitted (FEB-2026) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   ALTERNATIVE SPLICING, TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=12954765; DOI=10.1093/nar/gkg735;
RA   Berg A., Meza T.J., Mahic M., Thorstensen T., Kristiansen K., Aalen R.B.;
RT   "Ten members of the Arabidopsis gene family encoding methyl-CpG-binding
RT   domain proteins are transcriptionally active and at least one, AtMBD11, is
RT   crucial for normal development.";
RL   Nucleic Acids Res. 31:5291-5304(2003).
RN   [5]
RP   GENE FAMILY.
RX   PubMed=15888682; DOI=10.1104/pp.105.060566;
RA   Springer N.M., Kaeppler S.M.;
RT   "Evolutionary divergence of monocot and dicot methyl-CpG-binding domain
RT   proteins.";
RL   Plant Physiol. 138:92-104(2005).
RN   [6]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=16623890; DOI=10.1111/j.1365-313x.2006.02691.x;
RA   Peng M., Cui Y., Bi Y.-M., Rothstein S.J.;
RT   "AtMBD9: a protein with a methyl-CpG-binding domain regulates flowering
RT   time and shoot branching in Arabidopsis.";
RL   Plant J. 46:282-296(2006).
RN   [7]
RP   REVIEW.
RX   PubMed=17208509; DOI=10.1016/j.tplants.2006.12.004;
RA   Zemach A., Grafi G.;
RT   "Methyl-CpG-binding domain proteins in plants: interpreters of DNA
RT   methylation.";
RL   Trends Plant Sci. 12:80-85(2007).
RN   [8]
RP   FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, AND TISSUE
RP   SPECIFICITY.
RX   PubMed=19419532; DOI=10.1111/j.1365-313x.2009.03860.x;
RA   Yaish M.W.F., Peng M., Rothstein S.J.;
RT   "AtMBD9 modulates Arabidopsis development through the dual epigenetic
RT   pathways of DNA methylation and histone acetylation.";
RL   Plant J. 59:123-135(2009).
CC   -!- FUNCTION: Probable transcriptional regulator that acts as a histone
CC       acetyltransferase. Mediates the acetylation of histone H3 and H4 of
CC       target loci (e.g. FLC). Involved in an auxin-independent regulation of
CC       shoot branching and flowering time. {ECO:0000269|PubMed:16623890,
CC       ECO:0000269|PubMed:19419532}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L-lysyl-[protein] + acetyl-CoA = N(6)-acetyl-L-lysyl-[protein]
CC         + CoA + H(+); Xref=Rhea:RHEA:45948, Rhea:RHEA-COMP:9752, Rhea:RHEA-
CC         COMP:10731, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57287,
CC         ChEBI:CHEBI:57288, ChEBI:CHEBI:61930; EC=2.3.1.48;
CC   -!- SUBUNIT: Interacts with histone H4.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19419532}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q9SGH2-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q9SGH2-2; Sequence=Not described;
CC   -!- TISSUE SPECIFICITY: Expressed in leaves, buds, flowers and stems.
CC       {ECO:0000269|PubMed:12954765, ECO:0000269|PubMed:19419532}.
CC   -!- DOMAIN: The methyl-CpG-binding domain (MBD) functions both in binding
CC       to methylated DNA and in protein interactions. {ECO:0000250}.
CC   -!- DISRUPTION PHENOTYPE: Over-methylated genomic DNA. Increased shoot
CC       branching and reduced transcription of FLC leading to early flowering,
CC       associated with a decrease in the acetylation level in histone H3 and
CC       H4 of FLC chromatin. {ECO:0000269|PubMed:16623890,
CC       ECO:0000269|PubMed:19419532}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAF01531.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AC009325; AAF01531.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AC010870; AAF24616.1; -; Genomic_DNA.
DR   EMBL; CP002686; AEE73669.1; -; Genomic_DNA.
DR   EMBL; OZ408685; CAO7039260.1; -; Genomic_DNA.
DR   RefSeq; NP_186795.1; NM_111012.4. [Q9SGH2-1]
DR   AlphaFoldDB; Q9SGH2; -.
DR   SMR; Q9SGH2; -.
DR   BioGRID; 6465; 3.
DR   FunCoup; Q9SGH2; 2077.
DR   STRING; 3702.Q9SGH2; -.
DR   iPTMnet; Q9SGH2; -.
DR   PaxDb; 3702-Q9SGH2; -.
DR   ProteomicsDB; 238318; -. [Q9SGH2-1]
DR   GeneID; 821132; -.
DR   KEGG; ath:AT3G01460; -.
DR   Araport; AT3G01460; -.
DR   TAIR; AT3G01460; MBD9.
DR   eggNOG; ENOG502QW8S; Eukaryota.
DR   HOGENOM; CLU_234476_0_0_1; -.
DR   InParanoid; Q9SGH2; -.
DR   OMA; WTYYETE; -.
DR   OrthoDB; 1903104at2759; -.
DR   PhylomeDB; Q9SGH2; -.
DR   PRO; PR:Q9SGH2; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   ExpressionAtlas; Q9SGH2; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR   GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR   GO; GO:0000812; C:Swr1 complex; IDA:TAIR.
DR   GO; GO:0004402; F:histone acetyltransferase activity; IDA:UniProtKB.
DR   GO; GO:0042393; F:histone binding; IPI:UniProtKB.
DR   GO; GO:0008327; F:methyl-CpG binding; ISS:TAIR.
DR   GO; GO:0040029; P:epigenetic regulation of gene expression; IDA:UniProtKB.
DR   GO; GO:0048573; P:photoperiodism, flowering; IMP:TAIR.
DR   GO; GO:0006355; P:regulation of DNA-templated transcription; IMP:TAIR.
DR   GO; GO:0010223; P:secondary shoot formation; IMP:TAIR.
DR   CDD; cd15519; PHD1_Lid2p_like; 1.
DR   FunFam; 3.30.160.360:FF:000013; Methyl-CpG-binding domain 9; 1.
DR   Gene3D; 3.30.160.360; -; 1.
DR   Gene3D; 1.20.920.10; Bromodomain-like; 1.
DR   Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 2.
DR   InterPro; IPR036427; Bromodomain-like_sf.
DR   InterPro; IPR016177; DNA-bd_dom_sf.
DR   InterPro; IPR061860; DUF8799.
DR   InterPro; IPR003889; FYrich_C.
DR   InterPro; IPR003888; FYrich_N.
DR   InterPro; IPR001739; Methyl_CpG_DNA-bd.
DR   InterPro; IPR028942; WHIM1_dom.
DR   InterPro; IPR028941; WHIM2_dom.
DR   InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR   InterPro; IPR011011; Znf_FYVE_PHD.
DR   InterPro; IPR001965; Znf_PHD.
DR   InterPro; IPR019787; Znf_PHD-finger.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   PANTHER; PTHR47162:SF8; METHYL-CPG-BINDING DOMAIN-CONTAINING PROTEIN 9; 1.
DR   PANTHER; PTHR47162; OS02G0192300 PROTEIN; 1.
DR   Pfam; PF31066; DUF8799; 1.
DR   Pfam; PF05965; FYRC; 1.
DR   Pfam; PF05964; FYRN; 1.
DR   Pfam; PF01429; MBD; 1.
DR   Pfam; PF00628; PHD; 2.
DR   Pfam; PF15612; WHIM1; 1.
DR   Pfam; PF15613; WSD; 1.
DR   SMART; SM00249; PHD; 2.
DR   SUPFAM; SSF54171; DNA-binding domain; 1.
DR   SUPFAM; SSF57903; FYVE/PHD zinc finger; 2.
DR   PROSITE; PS50014; BROMODOMAIN_2; 1.
DR   PROSITE; PS51543; FYRC; 1.
DR   PROSITE; PS51542; FYRN; 1.
DR   PROSITE; PS50982; MBD; 1.
DR   PROSITE; PS01359; ZF_PHD_1; 2.
DR   PROSITE; PS50016; ZF_PHD_2; 2.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Bromodomain; Coiled coil; DNA-binding; Metal-binding;
KW   Nucleus; Reference proteome; Repeat; Transcription;
KW   Transcription regulation; Transferase; Zinc; Zinc-finger.
FT   CHAIN           1..2176
FT                   /note="Methyl-CpG-binding domain-containing protein 9"
FT                   /id="PRO_0000405285"
FT   DOMAIN          258..327
FT                   /note="MBD"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT   DOMAIN          403..456
FT                   /note="FYR N-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00875"
FT   DOMAIN          550..698
FT                   /note="FYR C-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00876"
FT   REPEAT          1098..1137
FT                   /note="Pumilio"
FT   DOMAIN          1130..1245
FT                   /note="Bromo"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00035"
FT   ZN_FING         83..133
FT                   /note="PHD-type 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   ZN_FING         86..131
FT                   /note="RING-type 1; degenerate"
FT   ZN_FING         1287..1337
FT                   /note="PHD-type 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   ZN_FING         1290..1335
FT                   /note="RING-type 2; degenerate"
FT   REGION          1..20
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          28..85
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1472..1553
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1565..1595
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          2136..2176
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          491..511
FT                   /evidence="ECO:0000255"
FT   COILED          1251..1273
FT                   /evidence="ECO:0000255"
FT   COILED          1410..1437
FT                   /evidence="ECO:0000255"
FT   COILED          1588..1628
FT                   /evidence="ECO:0000255"
FT   MOTIF           914..921
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   MOTIF           1124..1131
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   MOTIF           1256..1263
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   MOTIF           1337..1344
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   MOTIF           1761..1768
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   COMPBIAS        1..13
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1492..1513
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1523..1532
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1585..1595
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   2176 AA;  240431 MW;  05DBD955D895C3D5 CRC64;
     MEPTDSTNEQ LGDTKTAAVK EESRSFLGID LNEIPTGATL GGGCTAGQDD DGEYEPVEVV
     RSIHDNPDPA PGAPAEVPEP DRDASCGACG RPESIELVVV CDACERGFHM SCVNDGVEAA
     PSADWMCSDC RTGGERSKLW PLGVKSKLIL DMNASPPSDA EGYGAEETSD SRKHMLASSS
     CIGNSFDYAM MHSSFSSLGR GHASLEASGL MSRNTKMSMD ALGSHNLGFG FPLNLNNSSL
     PMRFPSLDPS ELFLQNLRHF ISERHGVLED GWRVEFRQPL NGYQLCAVYC APNGKTFSSI
     QEVACYLGLA INGNYSCMDA EIRNENSLLQ ERLHTPKRRK TSRWPNNGFP EQKGSSVSAQ
     LRRFPFNGQT MSPFAVKSGT HFQAGGSLSS GNNGCGCEEA KNGCPMQFED FFVLSLGRID
     IRQSYHNVNV IYPIGYKSCW HDKITGSLFT CEVSDGNSGP IFKVTRSPCS KSFIPAGSTV
     FSCPKIDEMV EQNSDKLSNR RDSTQERDDD ASVEILLSEH CPPLGDDILS CLREKSFSKT
     VNSLRSEVDS SRVDFDKNLS YDQDHGVEIG DIVVEEDSLS DAWKKVSQKL VDACSIVLKQ
     KGTLNFLCKH VDRETSEINW DTMNEKDNVI LSLSKFCCSL APCSVTCGEK DKSEFAAVVD
     ALSRWLDQNR FGLDADFVQE MIEHMPGAES CTNYRTLKSR SSSSVPITVA EGALVVKPKG
     GENVKDEVFG EISRKAKKPK LNGGHGVRNL HPPPGRPMCL RLPPGLVGDF LQVSEVFWRF
     HEILGFEEAF SPENLEQELI NPVFDGLFLD KPGKDDKRSE INFTDKDSTA TKLFSLFDES
     RQPFPAKNTS ASELKEKKAG DSSDFKISDS SRGSCVGALL TRAHISLLQV LICELQSKVA
     AFVDPNFDSG ESRSRRGRKK DDSTLSAKRN KLHMLPVNEF TWPELARRYI LSLLSMDGNL
     ESAEIAARES GKVFRCLQGD GGLLCGSLTG VAGMEADSML LAEAIKKISG SLTSENDVLS
     VEDDDSDGLD ATETNTCSGD IPEWAQVLEP VKKLPTNVGT RIRKCVYEAL ERNPPEWAKK
     ILEHSISKEI YKGNASGPTK KAVLSLLADI RGGDLVQRSI KGTKKRTYIS VSDVIMKKCR
     AVLRGVAAAD EDKVLCTLLG RKLLNSSDND DDGLLGSPAM VSRPLDFRTI DLRLAAGAYD
     GSTEAFLEDV LELWSSIRVM YADQPDCVDL VATLSEKFKS LYEAEVVPLV QKLKDYRKLE
     CLSAEMKKEI KDIVVSVNKL PKAPWDEGVC KVCGVDKDDD SVLLCDTCDA EYHTYCLNPP
     LIRIPDGNWY CPSCVIAKRM AQEALESYKL VRRRKGRKYQ GELTRASMEL TAHLADVMEE
     KDYWEFSAEE RILLLKLLCD ELLSSSLVHQ HLEQCAEAII EMQQKLRSLS SEWKNAKMRQ
     EFLTAKLAKV EPSILKEVGE PHNSSYFADQ MGCDPQPQEG VGDGVTRDDE TSSTAYLNKN
     QGKSPLETDT QPGESHVNFG ESKISSPETI SSPGRHELPI ADTSPLVTDN LPEKDTSETL
     LKSVGRNHET HSPNSNAVEL PTAHDASSQA SQELQACQQD LSATSNEIQN LQQSIRSIES
     QLLKQSIRRD FLGTDASGRL YWGCCFPDEN PRILVDGSIS LQKPVQADLI GSKVPSPFLH
     TVDHGRLRLS PWTYYETETE ISELVQWLHD DDLKERDLRE SILWWKRLRY GDVQKEKKQA
     QNLSAPVFAT GLETKAAMSM EKRYGPCIKL EMETLKKRGK KTKVAEREKL CRCECLESIL
     PSMIHCLICH KTFASDDEFE DHTESKCIPY SLATEEGKDI SDSSKAKESL KSDYLNVKSS
     AGKDVAEISN VSELDSGLIR YQEEESISPY HFEEICSKFV TKDCNRDLVK EIGLISSNGI
     PTFLPSSSTH LNDSVLISAK SNKPDGGDSG DQVIFAGPET NVEGLNSESN MSFDRSVTDS
     HGGPLDKPSG LGFGFSEQKN KKSSGSGLKS CCVVPQAALK RVTGKALPGF RFLKTNLLDM
     DVALPEEALR PSKSHPNRRR AWRVFVKSSQ SIYELVQATI VVEDMIKTEY LKNEWWYWSS
     LSAAAKISTL SALSVRIFSL DAAIIYDKPI TPSNPIDETK PIISLPDQKS QPVSDSQERS
     SRVRRSGKKR KEPEGS
//