ID SET1_CAEEL Reviewed; 1507 AA. AC Q18221; Q95QU6; Q95QU7; DT 23-APR-2003, integrated into UniProtKB/Swiss-Prot. DT 23-APR-2003, sequence version 2. DT 27-MAR-2024, entry version 163. DE RecName: Full=Histone-lysine N-methyltransferase set-2; DE EC=2.1.1.354 {ECO:0000250|UniProtKB:P38827}; DE AltName: Full=SET domain-containing protein 2; GN Name=set-2; ORFNames=C26E6.9; OS Caenorhabditis elegans. OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; OC Caenorhabditis. OX NCBI_TaxID=6239; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND ALTERNATIVE SPLICING. RC STRAIN=Bristol N2; 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] RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND ALTERNATIVE RP SPLICING. RX PubMed=11729150; DOI=10.1093/genetics/159.3.1019; RA Xu L., Strome S.; RT "Depletion of a novel SET-domain protein enhances the sterility of mes-3 RT and mes-4 mutants of Caenorhabditis elegans."; RL Genetics 159:1019-1029(2001). RN [3] RP FUNCTION. RX PubMed=12242227; DOI=10.1093/genetics/162.1.113; RA Colaiacovo M.P., Stanfield G.M., Reddy K.C., Reinke V., Kim S.K., RA Villeneuve A.M.; RT "A targeted RNAi screen for genes involved in chromosome morphogenesis and RT nuclear organization in the Caenorhabditis elegans germline."; RL Genetics 162:113-128(2002). RN [4] RP FUNCTION. RX PubMed=12724425; DOI=10.1128/mcb.23.10.3681-3691.2003; RA Jedrusik M.A., Schulze E.; RT "Telomeric position effect variegation in Saccharomyces cerevisiae by RT Caenorhabditis elegans linker histones suggests a mechanistic connection RT between germ line and telomeric silencing."; RL Mol. Cell. Biol. 23:3681-3691(2003). RN [5] RP FUNCTION. RX PubMed=17967446; DOI=10.1016/j.ydbio.2007.09.035; RA Simonet T., Dulermo R., Schott S., Palladino F.; RT "Antagonistic functions of SET-2/SET1 and HPL/HP1 proteins in C. elegans RT development."; RL Dev. Biol. 312:367-383(2007). RN [6] RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE. RX PubMed=20555324; DOI=10.1038/nature09195; RA Greer E.L., Maures T.J., Hauswirth A.G., Green E.M., Leeman D.S., RA Maro G.S., Han S., Banko M.R., Gozani O., Brunet A.; RT "Members of the H3K4 trimethylation complex regulate lifespan in a RT germline-dependent manner in C. elegans."; RL Nature 466:383-387(2010). RN [7] RP FUNCTION. RX PubMed=22012258; DOI=10.1038/nature10572; RA Greer E.L., Maures T.J., Ucar D., Hauswirth A.G., Mancini E., Lim J.P., RA Benayoun B.A., Shi Y., Brunet A.; RT "Transgenerational epigenetic inheritance of longevity in Caenorhabditis RT elegans."; RL Nature 479:365-371(2011). RN [8] RP FUNCTION, CATALYTIC ACTIVITY, AND INTERACTION WITH WDR-5.1. RX PubMed=21527717; DOI=10.1073/pnas.1019290108; RA Xiao Y., Bedet C., Robert V.J., Simonet T., Dunkelbarger S., RA Rakotomalala C., Soete G., Korswagen H.C., Strome S., Palladino F.; RT "Caenorhabditis elegans chromatin-associated proteins SET-2 and ASH-2 are RT differentially required for histone H3 Lys 4 methylation in embryos and RT adult germ cells."; RL Proc. Natl. Acad. Sci. U.S.A. 108:8305-8310(2011). RN [9] RP FUNCTION, AND DISRUPTION PHENOTYPE. RX PubMed=25124442; DOI=10.1126/science.1255885; RA Zuryn S., Ahier A., Portoso M., White E.R., Morin M.C., Margueron R., RA Jarriault S.; RT "Sequential histone-modifying activities determine the robustness of RT transdifferentiation."; RL Science 345:826-829(2014). RN [10] RP FUNCTION, AND DISRUPTION PHENOTYPE. RX PubMed=28379943; DOI=10.1038/nature21686; RA Han S., Schroeder E.A., Silva-Garcia C.G., Hebestreit K., Mair W.B., RA Brunet A.; RT "Mono-unsaturated fatty acids link H3K4me3 modifiers to C. elegans RT lifespan."; RL Nature 544:185-190(2017). RN [11] {ECO:0000305} RP IDENTIFICATION IN THE SET2 COMPLEX. RX PubMed=31602465; DOI=10.1093/nar/gkz880; RA Beurton F., Stempor P., Caron M., Appert A., Dong Y., Chen R.A., Cluet D., RA Coute Y., Herbette M., Huang N., Polveche H., Spichty M., Bedet C., RA Ahringer J., Palladino F.; RT "Physical and functional interaction between SET1/COMPASS complex component RT CFP-1 and a Sin3S HDAC complex in C. elegans."; RL Nucleic Acids Res. 47:11164-11180(2019). CC -!- FUNCTION: Catalytic component of the COMPASS (Set1C) complex that CC specifically mono-, di- and trimethylates histone H3 to form CC H3K4me1/2/3 (PubMed:21527717, PubMed:20555324). Binds RNAs which might CC negatively affect its histone methyltransferase activity (By CC similarity). COMPASS recognizes ubiquitinated H2B on one face of the CC nucleosome which stimulates the methylation of H3 on the opposing face CC (By similarity). H3 'Lys-4' methylation represents a specific tag for CC epigenetic transcriptional activation (PubMed:21527717). Implicated in CC the epigenetic inheritance of lifespan over several generations CC (PubMed:22012258). Acts in the germline to limit the longevity of the CC soma, probably by regulating a lipid metabolism pathway that signals CC from the germline to the intestine, thereby preventing accumulation of CC mono-unsaturated fatty acids (PubMed:20555324, PubMed:28379943). CC Methylation in the germline is required for germline development and CC fertility, possibly by ensuring genome stability (PubMed:21527717, CC PubMed:12242227). May act redundantly with mes-3 and mes-4 proteins in CC the development of a fertile germline (PubMed:11729150). Required for CC RNAi (PubMed:17967446). Functions as an antagonist of hpl-1 and hpl-2 CC activity in growth and somatic gonad development (PubMed:17967446). CC Cooperates with jmjd-3.1 and egl-27 to ensure robust CC transdifferentiation of the Y rectal cell to the PDA motor neuron CC during larval development (PubMed:25124442). CC {ECO:0000250|UniProtKB:P38827, ECO:0000269|PubMed:11729150, CC ECO:0000269|PubMed:12242227, ECO:0000269|PubMed:12724425, CC ECO:0000269|PubMed:17967446, ECO:0000269|PubMed:20555324, CC ECO:0000269|PubMed:21527717, ECO:0000269|PubMed:22012258, CC ECO:0000269|PubMed:25124442, ECO:0000269|PubMed:28379943}. CC -!- CATALYTIC ACTIVITY: CC Reaction=L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + CC N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L- CC homocysteine; Xref=Rhea:RHEA:60260, Rhea:RHEA-COMP:15537, Rhea:RHEA- CC COMP:15547, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.354; CC Evidence={ECO:0000250|UniProtKB:P38827}; CC -!- CATALYTIC ACTIVITY: CC Reaction=N(6)-methyl-L-lysyl(4)-[histone H3] + S-adenosyl-L-methionine CC = H(+) + N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + S-adenosyl-L- CC homocysteine; Xref=Rhea:RHEA:60268, Rhea:RHEA-COMP:15540, Rhea:RHEA- CC COMP:15543, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, CC ChEBI:CHEBI:61929, ChEBI:CHEBI:61976; CC Evidence={ECO:0000269|PubMed:20555324, ECO:0000269|PubMed:21527717}; CC -!- CATALYTIC ACTIVITY: CC Reaction=N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + S-adenosyl-L- CC methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] CC + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60272, Rhea:RHEA- CC COMP:15537, Rhea:RHEA-COMP:15540, ChEBI:CHEBI:15378, CC ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961, CC ChEBI:CHEBI:61976; Evidence={ECO:0000269|PubMed:20555324, CC ECO:0000269|PubMed:21527717}; CC -!- SUBUNIT: Component of the Set1C/COMPASS complex (also known as the SET2 CC complex), which contains at least set-2, swd-2.1, cfp-1, rbbp-5, CC wdr-5.1, dpy-30 and ash-2. {ECO:0000269|PubMed:31602465}. CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11729150}. CC Note=Localized in mitotic and mid-late-stage meiotic nuclei but is CC undetectable in early pachytene nuclei. CC -!- ALTERNATIVE PRODUCTS: CC Event=Alternative splicing; Named isoforms=3; CC Name=a; Synonyms=L; CC IsoId=Q18221-1; Sequence=Displayed; CC Name=b; Synonyms=S; CC IsoId=Q18221-2; Sequence=VSP_007217, VSP_007218; CC Name=c; CC IsoId=Q18221-3; Sequence=VSP_038347; CC -!- TISSUE SPECIFICITY: Expressed in all cells of embryo. In L1 larva, it CC is predominantly expressed in Z2 and Z3 primordial germ cells. In CC adults, it is predominantly expressed in the germline. CC {ECO:0000269|PubMed:11729150}. CC -!- DEVELOPMENTAL STAGE: Expressed throughout embryogenesis. CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown results in disruption of CC invariant Y-to-PDA transdifferentiation (PubMed:25124442). Results in CC decreased trimethylation at 'Lys-4' of histone H3 (PubMed:20555324). CC Leads to an extension of lifespan (PubMed:20555324). Leads to a CC deregulation of fat metabolism and to an enrichment of mono-unsaturated CC fatty acids (PubMed:28379943). {ECO:0000269|PubMed:20555324, CC ECO:0000269|PubMed:25124442, ECO:0000269|PubMed:28379943}. CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase CC superfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}. 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; FO080680; CCD65735.1; -; Genomic_DNA. DR EMBL; FO080680; CCD65734.1; -; Genomic_DNA. DR EMBL; FO080680; CCD65736.1; -; Genomic_DNA. DR PIR; A88445; A88445. DR RefSeq; NP_498039.1; NM_065638.3. [Q18221-3] DR RefSeq; NP_498040.1; NM_065639.4. [Q18221-1] DR RefSeq; NP_498041.1; NM_065640.3. [Q18221-2] DR AlphaFoldDB; Q18221; -. DR SMR; Q18221; -. DR BioGRID; 40896; 4. DR ELM; Q18221; -. DR STRING; 6239.C26E6.9c.1; -. DR EPD; Q18221; -. DR PaxDb; 6239-C26E6-9c; -. DR PeptideAtlas; Q18221; -. DR EnsemblMetazoa; C26E6.9a.1; C26E6.9a.1; WBGene00004782. [Q18221-1] DR EnsemblMetazoa; C26E6.9b.1; C26E6.9b.1; WBGene00004782. [Q18221-2] DR EnsemblMetazoa; C26E6.9c.1; C26E6.9c.1; WBGene00004782. [Q18221-3] DR GeneID; 175662; -. DR KEGG; cel:CELE_C26E6.9; -. DR UCSC; C26E6.9a; c. elegans. [Q18221-1] DR AGR; WB:WBGene00004782; -. DR WormBase; C26E6.9a; CE27735; WBGene00004782; set-2. [Q18221-1] DR WormBase; C26E6.9b; CE01158; WBGene00004782; set-2. [Q18221-2] DR WormBase; C26E6.9c; CE27736; WBGene00004782; set-2. [Q18221-3] DR eggNOG; KOG1080; Eukaryota. DR GeneTree; ENSGT00940000169211; -. DR InParanoid; Q18221; -. DR OMA; YCTIPPK; -. DR OrthoDB; 5490909at2759; -. DR Reactome; R-CEL-3214841; PKMTs methylate histone lysines. DR Reactome; R-CEL-8936459; RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function. DR Reactome; R-CEL-9772755; Formation of WDR5-containing histone-modifying complexes. DR PRO; PR:Q18221; -. DR Proteomes; UP000001940; Chromosome III. DR Bgee; WBGene00004782; Expressed in germ line (C elegans) and 8 other cell types or tissues. DR GO; GO:0005634; C:nucleus; IDA:WormBase. DR GO; GO:0048188; C:Set1C/COMPASS complex; IBA:GO_Central. DR GO; GO:0042800; F:histone H3K4 methyltransferase activity; IDA:WormBase. DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW. DR GO; GO:0008340; P:determination of adult lifespan; IMP:WormBase. DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW. DR GO; GO:0060290; P:transdifferentiation; IMP:WormBase. DR CDD; cd19169; SET_SETD1; 1. DR Gene3D; 3.30.70.330; -; 1. DR Gene3D; 2.170.270.10; SET domain; 1. DR InterPro; IPR024657; COMPASS_Set1_N-SET. DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf. DR InterPro; IPR003616; Post-SET_dom. DR InterPro; IPR035979; RBD_domain_sf. DR InterPro; IPR000504; RRM_dom. DR InterPro; IPR044570; Set1-like. DR InterPro; IPR001214; SET_dom. DR InterPro; IPR046341; SET_dom_sf. DR InterPro; IPR037841; SET_SETD1A/B. DR PANTHER; PTHR45814; HISTONE-LYSINE N-METHYLTRANSFERASE SETD1; 1. DR PANTHER; PTHR45814:SF2; HISTONE-LYSINE N-METHYLTRANSFERASE SETD1; 1. DR Pfam; PF00076; RRM_1; 1. DR Pfam; PF00856; SET; 1. DR SMART; SM01291; N-SET; 1. DR SMART; SM00508; PostSET; 1. DR SMART; SM00360; RRM; 1. DR SMART; SM00317; SET; 1. DR SUPFAM; SSF54928; RNA-binding domain, RBD; 1. DR SUPFAM; SSF82199; SET domain; 1. DR PROSITE; PS50868; POST_SET; 1. DR PROSITE; PS50280; SET; 1. PE 1: Evidence at protein level; KW Alternative splicing; Chromatin regulator; Developmental protein; KW Methyltransferase; Nucleus; Reference proteome; RNA-binding; KW S-adenosyl-L-methionine; Transcription; Transcription regulation; KW Transferase. FT CHAIN 1..1507 FT /note="Histone-lysine N-methyltransferase set-2" FT /id="PRO_0000097695" FT DOMAIN 128..199 FT /note="RRM" FT DOMAIN 1368..1485 FT /note="SET" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190" FT DOMAIN 1491..1507 FT /note="Post-SET" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155" FT REGION 1..32 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 280..578 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 650..697 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 803..826 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 842..1058 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 1163..1199 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOTIF 1340..1345 FT /note="RxxxRR motif" FT /evidence="ECO:0000250|UniProtKB:P38827" FT COMPBIAS 293..319 FT /note="Pro residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 321..345 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 375..390 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 415..447 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 449..469 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 489..519 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 520..549 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 550..564 FT /note="Pro residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 803..823 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 850..866 FT /note="Basic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 871..909 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 910..941 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 942..973 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 974..990 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 991..1017 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 1018..1048 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 1164..1179 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 1484 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190" FT VAR_SEQ 1..768 FT /note="Missing (in isoform b)" FT /evidence="ECO:0000305" FT /id="VSP_007217" FT VAR_SEQ 769..831 FT /note="MDELSRKVAEDIRQQIMRQCFAALDEKLHLKAIADEEKRKKEREEKARQEAE FT KPSNHLIADMM -> MYNNSAPYLNHSSLNTVRKKVVTVRRVLPSLPPPPPPPPSLYPP FT CSVFKVPYIPQRVYRSINS (in isoform b)" FT /evidence="ECO:0000305" FT /id="VSP_007218" FT VAR_SEQ 831 FT /note="M -> MPSQ (in isoform c)" FT /evidence="ECO:0000305" FT /id="VSP_038347" SQ SEQUENCE 1507 AA; 171683 MW; E7D9689DA720C34A CRC64; MSTHDMNHHP PRKSHSKRDK PSSSNSGPKI ENHKCKWAWQ KVFETGKSFL RRDGFPQDCK SKEDFERIKR TGVRKTSENM LEDPRKNFES LQQSSVYQTN SFRNPRYLCR AHLRVDSYYC TIPPKREVSL FNMDDNCTEV LLRDFAKDCG KVEKAYVCIH PETKRHMKMA YVKFATVKEA HNFYSMYHAQ NLLATKCTPR IDPFLSILNE EYEVATNGQV LPILPDDLAS IDPSVLRDLR ANFLRDQNEK YELAMRNTYE DEGGMLSGVI MDTSDHYERD YTMDHDVGPS SMKMSPIPPP PIKEESPPPP PPPPVASVSN LAPVPSVQLP YYNNIQPSSS TMHMPEFRPT EPPPSYSRED PYRSTSRSSL SRHRNRSRSP SDGMDRSGRS SSRRTHRRPE SRNGSKNANG DVVKYETYKM EKRKIKYEGG NKKYEQVHIK ERTAVIRGKN QLENVSSESA SGSSSVDTYP DFSDEERKKK KRPKSPNRSK KDSRAFGWDS TDESDEDTRR RRSGRSQNRS SERKFQTTSS SSTRRELSST HTNSVPNLKS HETPPPPPPK GHPSVHLQTP YQHVQPQMIP ATYYNLPPQH MAPPPITTSL PPFCDFSQPP PGFTPTFKPI TNAPLPTPYQ ASNIPQPGLV QIAALSAAPE PFSSIPGPPP GPAPIQEDVG RAESPEKPSL SERFSGIFGP TQREEPAQVE VEYDYPLKHS ESHDDRHSLE DMDVEVSSDG ETVSNVEKIE CMEEKKRQDL ERIAIARTPI VKKCKKRMMD ELSRKVAEDI RQQIMRQCFA ALDEKLHLKA IADEEKRKKE REEKARQEAE KPSNHLIADM MTLYNNQSFA SSSRGFYRKQ KPIPKSHPKH QEHHHHAKAS VSTPVHSSST SRNSSVAPTP QRTVSTSSSS SSAATSARVS EDESDSDSTP GEVQRRKTSV LSNDKRRRRA SFSSTSIQSS PERQRDVSSS SRTSSSSSTS SMKQEETADE KSRKRKLIMS SDESSTTGST ATSVVSSRQS SLEPQQEKTD GEPPKKKSQT DFISERVSKI EGEERPLPEP VETSGPIIGD SSYLPYKIVH WEKAGIIEMN LPANSIRAHE YHPFTTEHCY FGIDDPRQPK IQIFDHSPCK SEPGSEPLKI TPAPWGPIDN VAETGPLIYM DVVTAPKTVQ KKQKPRKQVF EKDPYEYYEP PPTKRPAPPP RFKKTFKPRS EEEKKKIIGD CEDLPDLEDQ WYLRAALNEM QSEVKSADEL PWKKMLTFKE MLRSEDPLLR LNPIRSKKGL PDAFYEDEEL DGVIPVAAGC SRARPYEKMT MKQKRSLVRR PDNESHPTAI FSERDETAIR HQHLASKDMR LLQRRLLTSL GDANNDFFKI NQLKFRKKMI KFARSRIHGW GLYAMESIAP DEMIVEYIGQ TIRSLVAEER EKAYERRGIG SSYLFRIDLH HVIDATKRGN FARFINHSCQ PNCYAKVLTI EGEKRIVIYS RTIIKKGEEI TYDYKFPIED DKIDCLCGAK TCRGYLN //