SWIC1_CAEEL
ID SWIC1_CAEEL Reviewed; 446 AA.
AC Q09646;
DT 07-OCT-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=SWI/SNF chromatin-remodeling accessory subunit 1 {ECO:0000305};
DE AltName: Full=Abnormal HSN migration protein 3 {ECO:0000312|WormBase:ZK1128.5};
GN Name=ham-3 {ECO:0000312|WormBase:ZK1128.5};
GN Synonyms=swsn-2.1 {ECO:0000303|PubMed:23457234},
GN tag-246 {ECO:0000303|PubMed:23457234};
GN ORFNames=ZK1128.5 {ECO:0000312|WormBase:ZK1128.5};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239 {ECO:0000312|Proteomes:UP000001940};
RN [1] {ECO:0000312|Proteomes:UP000001940}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2 {ECO:0000312|Proteomes:UP000001940};
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [2] {ECO:0000305}
RP TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, AND
RP MUTAGENESIS OF 22-GLN--ASN-446.
RX PubMed=23457234; DOI=10.1534/genetics.112.148742;
RA Weinberg P., Flames N., Sawa H., Garriga G., Hobert O.;
RT "The SWI/SNF chromatin remodeling complex selectively affects multiple
RT aspects of serotonergic neuron differentiation.";
RL Genetics 194:189-198(2013).
RN [3] {ECO:0000305}
RP FUNCTION.
RX PubMed=24402584; DOI=10.1534/g3.113.009852;
RA Large E.E., Mathies L.D.;
RT "Caenorhabditis elegans SWI/SNF subunits control sequential developmental
RT stages in the somatic gonad.";
RL G3 (Bethesda) 4:471-483(2014).
RN [4] {ECO:0000305}
RP FUNCTION, IDENTIFICATION IN THE SWI/SNF COMPLEX, DISRUPTION PHENOTYPE, AND
RP MUTAGENESIS OF 22-GLN--ASN-446.
RX PubMed=26739451; DOI=10.1534/genetics.115.183533;
RA Ertl I., Porta-de-la-Riva M., Gomez-Orte E., Rubio-Pena K.,
RA Aristizabal-Corrales D., Cornes E., Fontrodona L., Osteikoetxea X.,
RA Ayuso C., Askjaer P., Cabello J., Ceron J.;
RT "Functional Interplay of Two Paralogs Encoding SWI/SNF Chromatin-Remodeling
RT Accessory Subunits During Caenorhabditis elegans Development.";
RL Genetics 202:961-975(2016).
RN [5] {ECO:0000305}
RP FUNCTION, INTERACTION WITH BLMP-1, AND DISRUPTION PHENOTYPE.
RX PubMed=32417234; DOI=10.1016/j.bbagrm.2020.194577;
RA Fong H.T., Hagen T., Inoue T.;
RT "LDB1 and the SWI/SNF complex participate in both transcriptional
RT activation and repression by Caenorhabditis elegans BLIMP1/PRDM1.";
RL Biochim. Biophys. Acta 1863:194577-194577(2020).
CC -!- FUNCTION: Involved in transcriptional activation and repression of
CC select genes by chromatin remodeling (alteration of DNA-nucleosome
CC topology). Component of SWI/SNF chromatin remodeling complexes that
CC carry out key enzymatic activities, changing chromatin structure by
CC altering DNA-histone contacts within a nucleosome in an ATP-dependent
CC manner (By similarity). Required for the blmp-1-mediated
CC transcriptional activation or repression of several hypodermal genes
CC such as bed-3 (PubMed:32417234). Involved in regulating
CC differentiation, migration and axon pathfinding of specific
CC serotonergic neurons (HSNs) (PubMed:26739451). Probably regulates vulva
CC development through the let-60/Ras pathway (PubMed:26739451). May be
CC involved in regulation of developmental processes in the embryo driven
CC by the Wnt pathway (PubMed:26739451). Involved in gonadogenesis
CC (PubMed:26739451, PubMed:24402584). {ECO:0000250|UniProtKB:Q96GM5,
CC ECO:0000269|PubMed:24402584, ECO:0000269|PubMed:26739451,
CC ECO:0000269|PubMed:32417234}.
CC -!- SUBUNIT: Component of the multiprotein chromatin-remodeling complexes
CC SWI/SNF: SWI/SNF-A (BAF), SWI/SNF-B (PBAF) and related complexes
CC (Probable). The canonical complex contains a catalytic subunit swsn-4,
CC core subunits swsn-1 and swsn-5, and accessory subunits swsn-3, swsn-6,
CC phf-10, dpff-1, swsn-9 and either ham-3/swsn-2.1 or swsn-2.2
CC (Probable). May interact with blmp-1 (PubMed:32417234).
CC {ECO:0000269|PubMed:32417234, ECO:0000305|PubMed:26739451}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q96GM5}.
CC -!- TISSUE SPECIFICITY: Broadly expressed in all cell types.
CC {ECO:0000269|PubMed:23457234}.
CC -!- DEVELOPMENTAL STAGE: First observed after gastrulation and persists
CC into the first larval stages and in the adult.
CC {ECO:0000269|PubMed:23457234}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown at the L1 larval stage
CC reduces brood size (PubMed:26739451). RNAi-mediated knockdown reduces
CC expression of tph-1, which encodes a component of the serotonin
CC synthesis pathway (PubMed:23457234). RNAi-mediated knockdown reduces
CC the level of bed-3 and col-124 mRNAs and increases the level of lin-29
CC mRNA (PubMed:32417234). Simultaneous knockouts of swsn-2.2 do not
CC survive beyond the L2 larval stage (PubMed:24402584). Simultaneous
CC RNAi-mediated knockdown of swsn-2.2 at the L1 larval stage causes
CC sterility, while at the L3 larval stage, causes embryonic lethality for
CC the progeny (PubMed:26739451). The sterile animals resulting from
CC simultaneous RNAi-mediated knockdown of swsn-2.2 at the L1 larval stage
CC develop smaller germ lines (PubMed:26739451). Simultaneous RNAi-
CC mediated knockdown of swsn-2.2 also results in vulva protrusion and
CC ectopic expression of egl-17 in cells derived from the vulval precursor
CC cells P5.p and P7.p (PubMed:26739451). {ECO:0000269|PubMed:23457234,
CC ECO:0000269|PubMed:24402584, ECO:0000269|PubMed:26739451,
CC ECO:0000269|PubMed:32417234}.
CC -!- SIMILARITY: Belongs to the SMARCD family. {ECO:0000305}.
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DR EMBL; BX284603; CAA87424.1; -; Genomic_DNA.
DR PIR; T27696; T27696.
DR RefSeq; NP_499250.1; NM_066849.4.
DR AlphaFoldDB; Q09646; -.
DR SMR; Q09646; -.
DR ComplexPortal; CPX-1030; BAF chromatin remodeling complex.
DR ComplexPortal; CPX-1031; PBAF chromatin remodeling complex.
DR IntAct; Q09646; 3.
DR STRING; 6239.ZK1128.5; -.
DR EPD; Q09646; -.
DR PaxDb; Q09646; -.
DR PeptideAtlas; Q09646; -.
DR EnsemblMetazoa; ZK1128.5.1; ZK1128.5.1; WBGene00044072.
DR GeneID; 176426; -.
DR KEGG; cel:CELE_ZK1128.5; -.
DR UCSC; ZK1128.5; c. elegans.
DR CTD; 176426; -.
DR WormBase; ZK1128.5; CE01687; WBGene00044072; ham-3.
DR eggNOG; KOG2570; Eukaryota.
DR GeneTree; ENSGT00970000196486; -.
DR HOGENOM; CLU_023529_0_2_1; -.
DR InParanoid; Q09646; -.
DR OMA; LMGIWEY; -.
DR OrthoDB; 1027566at2759; -.
DR PhylomeDB; Q09646; -.
DR Reactome; R-CEL-8939243; RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known.
DR Proteomes; UP000001940; Chromosome III.
DR Bgee; WBGene00044072; Expressed in pharyngeal muscle cell (C elegans) and 4 other tissues.
DR GO; GO:0005634; C:nucleus; HDA:WormBase.
DR GO; GO:0016514; C:SWI/SNF complex; ISS:WormBase.
DR GO; GO:0140297; F:DNA-binding transcription factor binding; IPI:UniProtKB.
DR GO; GO:0061629; F:RNA polymerase II-specific DNA-binding transcription factor binding; ISS:WormBase.
DR GO; GO:0003713; F:transcription coactivator activity; IMP:UniProtKB.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0003714; F:transcription corepressor activity; IMP:UniProtKB.
DR GO; GO:0006338; P:chromatin remodeling; IC:ComplexPortal.
DR GO; GO:0008340; P:determination of adult lifespan; IMP:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:UniProtKB.
DR GO; GO:2000781; P:positive regulation of double-strand break repair; IC:ComplexPortal.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:2000045; P:regulation of G1/S transition of mitotic cell cycle; IC:ComplexPortal.
DR GO; GO:0030071; P:regulation of mitotic metaphase/anaphase transition; IC:ComplexPortal.
DR GO; GO:2000819; P:regulation of nucleotide-excision repair; IC:ComplexPortal.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; ISS:WormBase.
DR Gene3D; 1.10.245.10; -; 1.
DR InterPro; IPR019835; SWIB_domain.
DR InterPro; IPR036885; SWIB_MDM2_dom_sf.
DR InterPro; IPR003121; SWIB_MDM2_domain.
DR Pfam; PF02201; SWIB; 1.
DR SMART; SM00151; SWIB; 1.
DR SUPFAM; SSF47592; SSF47592; 1.
DR PROSITE; PS51925; SWIB_MDM2; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..446
FT /note="SWI/SNF chromatin-remodeling accessory subunit 1"
FT /evidence="ECO:0000305"
FT /id="PRO_0000451154"
FT DOMAIN 220..297
FT /note="SWIB/MDM2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01273"
FT REGION 1..53
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 22..446
FT /note="Missing: In n1654; lethal at the restrictive
FT temperature of 25 degrees Celsius. Protruding vulva
FT phenotype observed in 26% of animals and abnormal folding
FT and/or overmigration of the gonad arms in 18% and 47%,
FT respectively. Abnormal migration and axonal pathfinding of
FT hermaphrodite specific neurons (HSN) during embryogenesis
FT and reduced expression of several genes encoding components
FT of the serotonin synthesis and transport pathways. Germ
FT lines are smaller. Expression of sem-4 and ham-2 is
FT severely affected in the HSNs, while unc-86 expression is
FT barely affected."
FT /evidence="ECO:0000269|PubMed:23457234,
FT ECO:0000269|PubMed:26739451"
SQ SEQUENCE 446 AA; 51690 MW; 10E4948F2CA68ADE CRC64;
MQTQARPPVP QGPRFNHPAT PQQVRRPINA PLPGQTAQIQ GNRGPQPPKK KKRYADKLIQ
PKVRELVPES QAYMDLLAFE QKLDSTITRK KIDVQEALKR PQKIKKRLRI YISHTFIAGK
EPEKEGDDAS VPMWELRVEG RLLDDMQHPT VGANPRPAPK RKFSSFFKSL VIELDKDIYG
PDNHLVEWHR TPQTNETDGF QVKRPGDRPV KCTILLLLDY QPMKFKLHPR LAKVLGIAAE
TRPRIIEALW QYIKTHKLQD PQDRDTINND LFLEQCFGVS KMRFMEIPQR LHQLLQQPDP
LVLNHIIQRP DDGQDKTSAC YDIDVELEDP VKQQMANFVH NQTNANDIQL LDQKIFDLVD
QINEMKLRRD FFLRFSNEPS GFIKKWVVSQ NSDLKTLTES SGDGESDRYA TTYSTTDTDE
GVSRYMYQKI QQKRAELEQS LGIRNN
