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Chromatin remodeling protein SHL (Protein SHORT LIFE)

 SHL_ARATH               Reviewed;         228 AA.
Q9FEN9; Q8L975; Q9SVI4;
09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
01-MAR-2001, sequence version 1.
23-MAY-2018, entry version 136.
RecName: Full=Chromatin remodeling protein SHL {ECO:0000305};
AltName: Full=Protein SHORT LIFE {ECO:0000303|PubMed:11129039};
Name=SHL {ECO:0000303|PubMed:11129039}; Synonyms=SHL1 {ECO:0000305};
OrderedLocusNames=At4g39100 {ECO:0000312|EMBL:AEE87017.1};
ORFNames=F19H22.200 {ECO:0000312|EMBL:CAB38830.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702 {ECO:0000312|EMBL:AAG21353.1};
[1]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DISRUPTION PHENOTYPE,
SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
STRAIN=cv. C24;
PubMed=11129039; DOI=10.1007/s004380000313;
Muessig C., Kauschmann A., Clouse S.D., Altmann T.;
"The Arabidopsis PHD-finger protein SHL is required for proper
development and fertility.";
Mol. Gen. Genet. 264:363-370(2000).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
Feldmann K.A.;
"Full-length cDNA from Arabidopsis thaliana.";
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
[6]
FUNCTION.
PubMed=15082927; DOI=10.1023/B:PLAN.0000023661.65248.4b;
Muessig C., Altmann T.;
"Changes in gene expression in response to altered SHL transcript
levels.";
Plant Mol. Biol. 53:805-820(2003).
[7]
FUNCTION, MUTAGENESIS OF TRP-163, DISRUPTION PHENOTYPE, INTERACTION
WITH HISTONE AND HDA6, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
STRAIN=cv. Columbia, and cv. Landsberg erecta;
PubMed=25281686; DOI=10.1105/tpc.114.130781;
Lopez-Gonzalez L., Mouriz A., Narro-Diego L., Bustos R.,
Martinez-Zapater J.M., Jarillo J.A., Pineiro M.;
"Chromatin-dependent repression of the Arabidopsis floral integrator
genes involves plant specific PHD-containing proteins.";
Plant Cell 26:3922-3938(2014).
-!- FUNCTION: Chromatin remodeling factor that binds to methylated
histone (e.g. H3K4me2/3) to prevent their acetylation (e.g.
H3K9K14Ac), likely by recruiting histone deacetylase (HDAC)
complexes, and thus regulate the transcription of target genes
(PubMed:25281686). Required during development and for fertility,
probably by modulating developmental gene expression
(PubMed:11129039, PubMed:15082927, PubMed:25281686). Promotes
development speed, but at fitness cost (PubMed:11129039). Involved
in the chromatin-mediated repression of floral initiation and
controls genes regulating flowering. Negatively regulates the
expression of the floral integrator SOC1, by preventing high
levels of H3 acetylation, thus maintaining an inactive chromatin
conformation (PubMed:25281686). {ECO:0000269|PubMed:11129039,
ECO:0000269|PubMed:15082927, ECO:0000269|PubMed:25281686}.
-!- SUBUNIT: Recognizes di- and trimethylated histone H3 at lysine 4.
Interacts with HDA6. {ECO:0000269|PubMed:25281686}.
-!- INTERACTION:
Q8VZJ1-1:ATXR5; NbExp=3; IntAct=EBI-4458733, EBI-15200822;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00768, ECO:0000269|PubMed:11129039}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=1;
Comment=Additional isoforms may exist. {ECO:0000305};
Name=1;
IsoId=Q9FEN9-1; Sequence=Displayed;
-!- TISSUE SPECIFICITY: Expressed ubiquitously (PubMed:25281686).
Mostly expressed in roots, stems, leaves and flowers, and, to a
lower extent, in siliques (PubMed:11129039).
{ECO:0000269|PubMed:11129039, ECO:0000269|PubMed:25281686}.
-!- DEVELOPMENTAL STAGE: Expressed at all stages of development, from
seedlings to adult reproductive phase.
{ECO:0000269|PubMed:11129039, ECO:0000269|PubMed:25281686}.
-!- DISRUPTION PHENOTYPE: In antisense plants, dwarf phenotype
characterized by stunted axis, dark-green leaves, compact rosette
structure, less small leaves, fewer flowers and seeds, and
associated with a delayed development and late flowering
(PubMed:11129039). In shl-2, acceleration of flowering, especially
in short-days (SD), associated with a shorter adult vegetative
phase. Other developmental defects include premature senescence,
smaller leaves and siliques. Higher H3K9K14 acetylation in the
genomic region of the SOC1 locus (PubMed:25281686).
{ECO:0000269|PubMed:11129039, ECO:0000269|PubMed:25281686}.
-!- SIMILARITY: Belongs to the SHL1/EBS protein family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAB38830.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=CAB80573.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; AF277453; AAG21353.1; -; mRNA.
EMBL; AL035679; CAB38830.1; ALT_SEQ; Genomic_DNA.
EMBL; AL161594; CAB80573.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002687; AEE87017.1; -; Genomic_DNA.
EMBL; AY050934; AAK93611.1; -; mRNA.
EMBL; AY079396; AAL85127.1; -; mRNA.
EMBL; AY088603; AAM66132.1; -; mRNA.
PIR; H85462; H85462.
PIR; T06070; T06070.
RefSeq; NP_568053.1; NM_120070.3. [Q9FEN9-1]
UniGene; At.47993; -.
UniGene; At.70103; -.
ProteinModelPortal; Q9FEN9; -.
SMR; Q9FEN9; -.
IntAct; Q9FEN9; 7.
STRING; 3702.AT4G39100.1; -.
iPTMnet; Q9FEN9; -.
PaxDb; Q9FEN9; -.
PRIDE; Q9FEN9; -.
EnsemblPlants; AT4G39100.1; AT4G39100.1; AT4G39100. [Q9FEN9-1]
GeneID; 830065; -.
Gramene; AT4G39100.1; AT4G39100.1; AT4G39100. [Q9FEN9-1]
KEGG; ath:AT4G39100; -.
Araport; AT4G39100; -.
TAIR; locus:2120252; AT4G39100.
eggNOG; KOG1632; Eukaryota.
eggNOG; KOG1886; Eukaryota.
eggNOG; ENOG4111Y07; LUCA.
HOGENOM; HOG000264809; -.
OMA; CEECSPQ; -.
OrthoDB; EOG09360L2V; -.
PhylomeDB; Q9FEN9; -.
PRO; PR:Q9FEN9; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; Q9FEN9; baseline and differential.
GO; GO:0000785; C:chromatin; IBA:GO_Central.
GO; GO:0005677; C:chromatin silencing complex; IBA:GO_Central.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0003682; F:chromatin binding; IBA:GO_Central.
GO; GO:0003700; F:DNA binding transcription factor activity; ISS:TAIR.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0035064; F:methylated histone binding; IDA:UniProtKB.
GO; GO:0000976; F:transcription regulatory region sequence-specific DNA binding; IDA:UniProtKB.
GO; GO:0006325; P:chromatin organization; IMP:UniProtKB.
GO; GO:0006342; P:chromatin silencing; IBA:GO_Central.
GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
GO; GO:0031507; P:heterochromatin assembly; IBA:GO_Central.
GO; GO:0035067; P:negative regulation of histone acetylation; IMP:UniProtKB.
GO; GO:0009791; P:post-embryonic development; IMP:UniProtKB.
GO; GO:2000028; P:regulation of photoperiodism, flowering; IMP:UniProtKB.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:UniProtKB.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
InterPro; IPR001025; BAH_dom.
InterPro; IPR019786; Zinc_finger_PHD-type_CS.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR001965; Znf_PHD.
InterPro; IPR019787; Znf_PHD-finger.
Pfam; PF01426; BAH; 1.
Pfam; PF00628; PHD; 1.
SMART; SM00439; BAH; 1.
SMART; SM00249; PHD; 1.
SUPFAM; SSF57903; SSF57903; 1.
PROSITE; PS51038; BAH; 1.
PROSITE; PS01359; ZF_PHD_1; 1.
PROSITE; PS50016; ZF_PHD_2; 1.
1: Evidence at protein level;
Alternative splicing; Chromatin regulator; Complete proteome;
Flowering; Metal-binding; Nucleus; Reference proteome; Transcription;
Transcription regulation; Zinc; Zinc-finger.
CHAIN 1 228 Chromatin remodeling protein SHL.
/FTId=PRO_0000434826.
DOMAIN 21 137 BAH. {ECO:0000255|PROSITE-
ProRule:PRU00370}.
ZN_FING 139 190 PHD-type. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
MOTIF 210 217 Nuclear localization signal.
{ECO:0000255|PROSITE-ProRule:PRU00768}.
MUTAGEN 163 163 W->A: Impaired H3K4me2/3 binding.
{ECO:0000269|PubMed:25281686}.
CONFLICT 107 107 S -> T (in Ref. 5; AAM66132).
{ECO:0000305}.
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


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