SHL_ARATH
ID SHL_ARATH Reviewed; 228 AA.
AC Q9FEN9; Q8L975; Q9SVI4;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 25-MAY-2022, entry version 154.
DE RecName: Full=Chromatin remodeling protein SHL {ECO:0000305};
DE AltName: Full=Protein SHORT LIFE {ECO:0000303|PubMed:11129039};
GN Name=SHL {ECO:0000303|PubMed:11129039}; Synonyms=SHL1 {ECO:0000305};
GN OrderedLocusNames=At4g39100 {ECO:0000312|EMBL:AEE87017.1};
GN ORFNames=F19H22.200 {ECO:0000312|EMBL:CAB38830.1};
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 [MRNA], FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. C24;
RX PubMed=11129039; DOI=10.1007/s004380000313;
RA Muessig C., Kauschmann A., Clouse S.D., Altmann T.;
RT "The Arabidopsis PHD-finger protein SHL is required for proper development
RT and fertility.";
RL Mol. Gen. Genet. 264:363-370(2000).
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 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 [4]
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 [5]
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 [6]
RP FUNCTION.
RX PubMed=15082927; DOI=10.1023/b:plan.0000023661.65248.4b;
RA Muessig C., Altmann T.;
RT "Changes in gene expression in response to altered SHL transcript levels.";
RL Plant Mol. Biol. 53:805-820(2003).
RN [7]
RP FUNCTION, MUTAGENESIS OF TRP-163, DISRUPTION PHENOTYPE, INTERACTION WITH
RP HISTONE AND HDA6, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=25281686; DOI=10.1105/tpc.114.130781;
RA Lopez-Gonzalez L., Mouriz A., Narro-Diego L., Bustos R.,
RA Martinez-Zapater J.M., Jarillo J.A., Pineiro M.;
RT "Chromatin-dependent repression of the Arabidopsis floral integrator genes
RT involves plant specific PHD-containing proteins.";
RL Plant Cell 26:3922-3938(2014).
RN [8]
RP INTERACTION WITH DEK3, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=cv. Columbia;
RX PubMed=25387881; DOI=10.1105/tpc.114.129254;
RA Waidmann S., Kusenda B., Mayerhofer J., Mechtler K., Jonak C.;
RT "A DEK domain-containing protein modulates chromatin structure and function
RT in Arabidopsis.";
RL Plant Cell 26:4328-4344(2014).
CC -!- FUNCTION: Chromatin remodeling factor that binds to methylated histone
CC (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely
CC by recruiting histone deacetylase (HDAC) complexes, and thus regulate
CC the transcription of target genes (PubMed:25281686). Required during
CC development and for fertility, probably by modulating developmental
CC gene expression (PubMed:11129039, PubMed:15082927, PubMed:25281686).
CC Promotes development speed, but at fitness cost (PubMed:11129039).
CC Involved in the chromatin-mediated repression of floral initiation and
CC controls genes regulating flowering. Negatively regulates the
CC expression of the floral integrator SOC1, by preventing high levels of
CC H3 acetylation, thus maintaining an inactive chromatin conformation
CC (PubMed:25281686). {ECO:0000269|PubMed:11129039,
CC ECO:0000269|PubMed:15082927, ECO:0000269|PubMed:25281686}.
CC -!- SUBUNIT: Recognizes di- and trimethylated histone H3 at lysine 4
CC (PubMed:25281686). Interacts with HDA6 (PubMed:25281686). Interacts
CC with DEK3 (PubMed:25387881). {ECO:0000269|PubMed:25281686,
CC ECO:0000269|PubMed:25387881}.
CC -!- INTERACTION:
CC Q9FEN9; Q8VZJ1-1: ATXR5; NbExp=3; IntAct=EBI-4458733, EBI-15200822;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:11129039}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=Additional isoforms may exist. {ECO:0000305};
CC Name=1;
CC IsoId=Q9FEN9-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed ubiquitously (PubMed:25281686). Mostly
CC expressed in roots, stems, leaves and flowers, and, to a lower extent,
CC in siliques (PubMed:11129039). {ECO:0000269|PubMed:11129039,
CC ECO:0000269|PubMed:25281686}.
CC -!- DEVELOPMENTAL STAGE: Expressed at all stages of development, from
CC seedlings to adult reproductive phase. {ECO:0000269|PubMed:11129039,
CC ECO:0000269|PubMed:25281686}.
CC -!- DISRUPTION PHENOTYPE: In antisense plants, dwarf phenotype
CC characterized by stunted axis, dark-green leaves, compact rosette
CC structure, less small leaves, fewer flowers and seeds, and associated
CC with a delayed development and late flowering (PubMed:11129039). In
CC shl-2, acceleration of flowering, especially in short-days (SD),
CC associated with a shorter adult vegetative phase. Other developmental
CC defects include premature senescence, smaller leaves and siliques.
CC Higher H3K9K14 acetylation in the genomic region of the SOC1 locus
CC (PubMed:25281686). {ECO:0000269|PubMed:11129039,
CC ECO:0000269|PubMed:25281686}.
CC -!- SIMILARITY: Belongs to the SHL1/EBS protein family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB38830.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80573.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF277453; AAG21353.1; -; mRNA.
DR EMBL; AL035679; CAB38830.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161594; CAB80573.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE87017.1; -; Genomic_DNA.
DR EMBL; AY050934; AAK93611.1; -; mRNA.
DR EMBL; AY079396; AAL85127.1; -; mRNA.
DR EMBL; AY088603; AAM66132.1; -; mRNA.
DR PIR; H85462; H85462.
DR PIR; T06070; T06070.
DR RefSeq; NP_568053.1; NM_120070.3. [Q9FEN9-1]
DR AlphaFoldDB; Q9FEN9; -.
DR SMR; Q9FEN9; -.
DR IntAct; Q9FEN9; 7.
DR STRING; 3702.AT4G39100.1; -.
DR iPTMnet; Q9FEN9; -.
DR PaxDb; Q9FEN9; -.
DR PRIDE; Q9FEN9; -.
DR ProteomicsDB; 232678; -. [Q9FEN9-1]
DR EnsemblPlants; AT4G39100.1; AT4G39100.1; AT4G39100. [Q9FEN9-1]
DR GeneID; 830065; -.
DR Gramene; AT4G39100.1; AT4G39100.1; AT4G39100. [Q9FEN9-1]
DR KEGG; ath:AT4G39100; -.
DR Araport; AT4G39100; -.
DR TAIR; locus:2120252; AT4G39100.
DR eggNOG; KOG1632; Eukaryota.
DR eggNOG; KOG1886; Eukaryota.
DR InParanoid; Q9FEN9; -.
DR OMA; CEECSPQ; -.
DR PhylomeDB; Q9FEN9; -.
DR PRO; PR:Q9FEN9; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9FEN9; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003682; F:chromatin binding; IEA:InterPro.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035064; F:methylated histone binding; IDA:UniProtKB.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IDA:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IMP:UniProtKB.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0035067; P:negative regulation of histone acetylation; IMP:UniProtKB.
DR GO; GO:0009791; P:post-embryonic development; IMP:UniProtKB.
DR GO; GO:2000028; P:regulation of photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP:TAIR.
DR Gene3D; 2.30.30.490; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR001025; BAH_dom.
DR InterPro; IPR043151; BAH_sf.
DR InterPro; IPR045205; EBS/SHL-like.
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; PTHR46364:SF7; PTHR46364:SF7; 1.
DR Pfam; PF01426; BAH; 1.
DR Pfam; PF00628; PHD; 1.
DR SMART; SM00439; BAH; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51038; BAH; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chromatin regulator; Flowering; Metal-binding;
KW Nucleus; Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..228
FT /note="Chromatin remodeling protein SHL"
FT /id="PRO_0000434826"
FT DOMAIN 21..137
FT /note="BAH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT ZN_FING 139..190
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 191..228
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 210..217
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 191..207
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 208..222
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 163
FT /note="W->A: Impaired H3K4me2/3 binding."
FT /evidence="ECO:0000269|PubMed:25281686"
FT CONFLICT 107
FT /note="S -> T (in Ref. 5; AAM66132)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 228 AA; 26122 MW; A800BC81E5B8390A CRC64;
MPKQKAPRKQ LKSYKLKHIN KSIQEGDAVL MRSSEPGKPS YVARVEAIET DARGSHAKVR
VRWYYRPEES IGGRRQFHGA KEVFLSDHFD FQSADTIEGK CKVHSFSSYT KLDSVGNDDF
FCRFEYNSTT GAFDPDRVTV FCKCEMPYNP DDLMVQCEEC SEWFHPSCIG TTIEEAKKPD
NFYCEECSPQ QQNLHNSNST SNNRDAKVNG KRSLEVTKSK NKHTKRPG
