ID CDYL_RAT Reviewed; 589 AA. AC Q6AYK9; DT 26-JUN-2007, integrated into UniProtKB/Swiss-Prot. DT 13-SEP-2004, sequence version 1. DT 24-JAN-2024, entry version 133. DE RecName: Full=Chromodomain Y-like protein {ECO:0000250|UniProtKB:Q9Y232}; DE Short=CDY-like {ECO:0000250|UniProtKB:Q9Y232}; DE AltName: Full=Crotonyl-CoA hydratase {ECO:0000250|UniProtKB:Q9Y232}; DE EC=4.2.1.- {ECO:0000250|UniProtKB:Q9Y232}; DE AltName: Full=Putative tubulin acetyltransferase Cdyl {ECO:0000305}; DE EC=2.3.1.- {ECO:0000305|PubMed:28681565}; GN Name=Cdyl {ECO:0000312|RGD:1549745}; OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; OC Murinae; Rattus. OX NCBI_TaxID=10116; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=Brown Norway; RX PubMed=15057822; DOI=10.1038/nature02426; RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., RA Mockrin S., Collins F.S.; RT "Genome sequence of the Brown Norway rat yields insights into mammalian RT evolution."; RL Nature 428:493-521(2004). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RC TISSUE=Testis; RX PubMed=15489334; DOI=10.1101/gr.2596504; RG The MGC Project Team; RT "The status, quality, and expansion of the NIH full-length cDNA project: RT the Mammalian Gene Collection (MGC)."; RL Genome Res. 14:2121-2127(2004). RN [3] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-82 AND SER-210, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=22673903; DOI=10.1038/ncomms1871; RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., RA Olsen J.V.; RT "Quantitative maps of protein phosphorylation sites across 14 different rat RT organs and tissues."; RL Nat. Commun. 3:876-876(2012). RN [4] RP PUTATIVE FUNCTION. RX PubMed=28681565; DOI=10.1002/cm.21381; RA Parab S., Dalvi V., Mylavaram S., Kishore A., Idicula-Thomas S., RA Sonawane S., Parte P.; RT "Tubulin acetylation: A novel functional avenue for CDYL in sperm."; RL Cytoskeleton 74:331-342(2017). RN [5] RP FUNCTION, TISSUE SPECIFICITY, AND REPRESSION BY NEURONAL ACTIVITY. RX PubMed=28842554; DOI=10.1038/s41467-017-00368-z; RA Liu Y., Lai S., Ma W., Ke W., Zhang C., Liu S., Zhang Y., Pei F., Li S., RA Yi M., Shu Y., Shang Y., Liang J., Huang Z.; RT "CDYL suppresses epileptogenesis in mice through repression of axonal RT Nav1.6 sodium channel expression."; RL Nat. Commun. 8:355-355(2017). RN [6] RP TISSUE SPECIFICITY, AND INDUCTION BY SOCIAL DEFEAT STRESS. RX PubMed=30665597; DOI=10.1016/j.biopsych.2018.11.025; RA Liu Y., Li M., Fan M., Song Y., Yu H., Zhi X., Xiao K., Lai S., Zhang J., RA Jin X., Shang Y., Liang J., Huang Z.; RT "Chromodomain Y-like Protein-Mediated Histone Crotonylation Regulates RT Stress-Induced Depressive Behaviors."; RL Biol. Psychiatry 85:635-649(2019). CC -!- FUNCTION: [Isoform 2]: Chromatin reader protein that recognizes and CC binds histone H3 trimethylated at 'Lys-9', dimethylated at 'Lys-27' and CC trimethylated at 'Lys-27' (H3K9me3, H3K27me2 and H3K27me3, CC respectively). Part of multimeric repressive chromatin complexes, where CC it is required for transmission and restoration of repressive histone CC marks, thereby preserving the epigenetic landscape. Required for CC chromatin targeting and maximal enzymatic activity of Polycomb CC repressive complex 2 (PRC2); acts as a positive regulator of PRC2 CC activity by bridging the pre-existing histone H3K27me3 and newly CC recruited PRC2 on neighboring nucleosomes. Acts as a corepressor for CC REST by facilitating histone-lysine N-methyltransferase EHMT2 CC recruitment and H3K9 dimethylation at REST target genes for repression CC (By similarity). Involved in X chromosome inactivation in females: CC recruited to Xist RNA-coated X chromosome and facilitates propagation CC of H3K9me2 by anchoring EHMT2 (By similarity). Promotes EZH2 CC accumulation and H3K27me3 methylation at DNA double strand breaks CC (DSBs), thereby facilitating transcriptional repression at sites of DNA CC damage and homology-directed repair of DSBs (By similarity). Required CC for neuronal migration during brain development by repressing CC expression of RHOA (By similarity). By repressing the expression of CC SCN8A, contributes to the inhibition of intrinsic neuronal excitability CC and epileptogenesis (PubMed:28842554). In addition to acting as a CC chromatin reader, acts as a hydro-lyase. Shows crotonyl-coA hydratase CC activity by mediating the conversion of crotonyl-CoA ((2E)-butenoyl- CC CoA) to beta-hydroxybutyryl-CoA (3-hydroxybutanoyl-CoA), thereby acting CC as a negative regulator of histone crotonylation (By similarity). CC Histone crotonylation is required during spermatogenesis; down- CC regulation of histone crotonylation by CDYL regulates the reactivation CC of sex chromosome-linked genes in round spermatids and histone CC replacement in elongating spermatids (By similarity). By regulating CC histone crotonylation and trimethylation of H3K27, may be involved in CC stress-induced depression-like behaviors, possibly by regulating VGF CC expression (By similarity). Displays acetyltransferase activity toward CC tubulin in vitro; such activity is however unsure in vivo and CC additional evidences would be required to confirm this result CC (PubMed:28681565). {ECO:0000250|UniProtKB:Q9WTK2, CC ECO:0000250|UniProtKB:Q9Y232, ECO:0000269|PubMed:28842554, CC ECO:0000305|PubMed:28681565}. CC -!- FUNCTION: [Isoform 1]: Not able to recognize and bind histone H3K9me3, CC histone H3K27me2 and histone H3K27me3, due to the presence of a N- CC terminal extension that inactivates the chromo domain. CC {ECO:0000250|UniProtKB:Q9Y232}. CC -!- CATALYTIC ACTIVITY: CC Reaction=3-hydroxybutanoyl-CoA = (2E)-butenoyl-CoA + H2O; CC Xref=Rhea:RHEA:45584, ChEBI:CHEBI:15377, ChEBI:CHEBI:57332, CC ChEBI:CHEBI:78611; Evidence={ECO:0000250|UniProtKB:Q9Y232}; CC -!- SUBUNIT: Forms multimers and multimerization is required for stable CC binding to chromatin (By similarity). Interacts with HDAC1 and HDAC2 CC via its C-terminal acetyl-CoA-binding domain (By similarity). Interacts CC with EZH2, EED, SUZ12, REST, EHMT1 and EHMT2. Part of a complex CC containing at least CDYL, REST, WIZ, SETB1, EHMT1 and EHMT2. Part of a CC complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2. CC Interacts with CHAF1A and CHAF1B; bridging the CAF-1 complex to the CC MCM2-7 (MCM) complex. Interacts with MCM3 and MCM5; bridging the CAF-1 CC complex to the MCM2-7 (MCM) complex (By similarity). Recruited to Xist CC RNA-coated X chromosome (By similarity). Interacts with EHMT2 and CC PRDM9; interaction only takes place when PRDM9 is bound to hotspot DNA CC (By similarity). {ECO:0000250|UniProtKB:Q9WTK2, CC ECO:0000250|UniProtKB:Q9Y232}. CC -!- SUBCELLULAR LOCATION: [Isoform 2]: Nucleus CC {ECO:0000250|UniProtKB:Q9Y232}. Chromosome CC {ECO:0000250|UniProtKB:Q9Y232}. Note=Recognizes and binds histone H3 CC trimethylated at 'Lys-9', dimethylated at 'Lys-27' and trimethylated at CC 'Lys-27' (H3K9me3, H3K27me2 and H3K27me3, respectively) on chromatin. CC Multimerization is required for chromatin-binding. Recruited to sites CC of DNA double strand breaks in a PARP1-dependent fashion (By CC similarity). {ECO:0000250|UniProtKB:Q9Y232}. CC -!- ALTERNATIVE PRODUCTS: CC Event=Alternative splicing; Named isoforms=2; CC Name=1; Synonyms=a {ECO:0000250|UniProtKB:Q9Y232}, CDYL1a CC {ECO:0000250|UniProtKB:Q9Y232}; CC IsoId=Q6AYK9-1; Sequence=Displayed; CC Name=2; Synonyms=b {ECO:0000250|UniProtKB:Q9Y232}, CDYL1b CC {ECO:0000250|UniProtKB:Q9Y232}; CC IsoId=Q6AYK9-2; Sequence=VSP_059157; CC -!- TISSUE SPECIFICITY: Expressed in the brain, with expression in the CC hippocampal dentate gyrus, CA1, striatum and cortex (at protein level) CC (PubMed:28842554). Expressed in the prelimbic cortex (PubMed:30665597). CC {ECO:0000269|PubMed:28842554, ECO:0000269|PubMed:30665597}. CC -!- INDUCTION: Down-regulated upon neuronal activity in response to an CC enriched environment, NMDA injection in the brain or seizures induced CC by kainic acid (at protein level) (PubMed:28842554). Up-regulated after CC social defeat stress (PubMed:30665597). {ECO:0000269|PubMed:28842554, CC ECO:0000269|PubMed:30665597}. CC -!- DOMAIN: The chromo domain recognizes and binds histone H3K9me3, histone CC H3K27me2 and histone H3K27me3. {ECO:0000250|UniProtKB:Q9Y232}. CC -!- DOMAIN: The acetyl-CoA-binding domain mediates crotonyl-coA hydratase CC activity (By similarity). The acetyl-CoA-binding domain is required for CC recruitment to sites of DNA double strand breaks and for binding to CC poly (ADP ribose) moieties (By similarity). CC {ECO:0000250|UniProtKB:Q9Y232}. CC -!- CAUTION: Acetyltransferase activity toward tubulin in vitro is unclear CC (PubMed:28681565). Crystallographic studies with the human protein CC demonstrated that it does not share any similarity with other CC acetyltransferases and instead forms a crotonase-like fold. CC {ECO:0000305|PubMed:28681565}. 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; AC117279; -; NOT_ANNOTATED_CDS; Genomic_DNA. DR EMBL; AC140751; -; NOT_ANNOTATED_CDS; Genomic_DNA. DR EMBL; BC079003; AAH79003.1; -; mRNA. DR RefSeq; NP_001014167.1; NM_001014145.1. [Q6AYK9-1] DR AlphaFoldDB; Q6AYK9; -. DR SMR; Q6AYK9; -. DR STRING; 10116.ENSRNOP00000048651; -. DR iPTMnet; Q6AYK9; -. DR PhosphoSitePlus; Q6AYK9; -. DR PaxDb; 10116-ENSRNOP00000048651; -. DR Ensembl; ENSRNOT00000100703.1; ENSRNOP00000095115.1; ENSRNOG00000032215.4. [Q6AYK9-2] DR Ensembl; ENSRNOT00055023066; ENSRNOP00055018708; ENSRNOG00055013448. [Q6AYK9-1] DR Ensembl; ENSRNOT00060016635; ENSRNOP00060012997; ENSRNOG00060009819. [Q6AYK9-1] DR Ensembl; ENSRNOT00065013023; ENSRNOP00065009604; ENSRNOG00065008216. [Q6AYK9-1] DR GeneID; 361237; -. DR KEGG; rno:361237; -. DR UCSC; RGD:1549745; rat. [Q6AYK9-1] DR AGR; RGD:1549745; -. DR CTD; 9425; -. DR RGD; 1549745; Cdyl. DR VEuPathDB; HostDB:ENSRNOG00000032215; -. DR eggNOG; KOG0016; Eukaryota. DR eggNOG; KOG1911; Eukaryota. DR GeneTree; ENSGT00940000155106; -. DR HOGENOM; CLU_009834_24_0_1; -. DR InParanoid; Q6AYK9; -. DR OrthoDB; 553487at2759; -. DR PhylomeDB; Q6AYK9; -. DR TreeFam; TF313375; -. DR PRO; PR:Q6AYK9; -. DR Proteomes; UP000002494; Chromosome 17. DR Bgee; ENSRNOG00000032215; Expressed in testis and 19 other cell types or tissues. DR GO; GO:0005694; C:chromosome; ISS:UniProtKB. DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB. DR GO; GO:0005634; C:nucleus; ISS:UniProtKB. DR GO; GO:0016746; F:acyltransferase activity; IEA:UniProtKB-KW. DR GO; GO:0003682; F:chromatin binding; ISS:UniProtKB. DR GO; GO:0120092; F:crotonyl-CoA hydratase activity; ISS:UniProtKB. DR GO; GO:0035064; F:methylated histone binding; ISS:UniProtKB. DR GO; GO:0030674; F:protein-macromolecule adaptor activity; ISO:RGD. DR GO; GO:0003714; F:transcription corepressor activity; ISS:UniProtKB. DR GO; GO:0120094; P:negative regulation of peptidyl-lysine crotonylation; ISS:UniProtKB. DR GO; GO:0060816; P:random inactivation of X chromosome; ISS:UniProtKB. DR GO; GO:0007286; P:spermatid development; ISS:UniProtKB. DR CDD; cd18634; CD_CDY; 1. DR CDD; cd06558; crotonase-like; 1. DR Gene3D; 2.40.50.40; -; 1. DR Gene3D; 1.10.12.10; Lyase 2-enoyl-coa Hydratase, Chain A, domain 2; 1. DR InterPro; IPR016197; Chromo-like_dom_sf. DR InterPro; IPR000953; Chromo/chromo_shadow_dom. DR InterPro; IPR023780; Chromo_domain. DR InterPro; IPR023779; Chromodomain_CS. DR InterPro; IPR029045; ClpP/crotonase-like_dom_sf. DR InterPro; IPR001753; Enoyl-CoA_hydra/iso. DR InterPro; IPR014748; Enoyl-CoA_hydra_C. DR PANTHER; PTHR43684; -; 1. DR PANTHER; PTHR43684:SF5; CHROMODOMAIN Y-LIKE PROTEIN; 1. DR Pfam; PF00385; Chromo; 1. DR Pfam; PF00378; ECH_1; 1. DR SMART; SM00298; CHROMO; 1. DR SUPFAM; SSF54160; Chromo domain-like; 1. DR SUPFAM; SSF52096; ClpP/crotonase; 1. DR PROSITE; PS00598; CHROMO_1; 1. DR PROSITE; PS50013; CHROMO_2; 1. DR Genevisible; Q6AYK9; RN. PE 1: Evidence at protein level; KW Acyltransferase; Alternative splicing; Chromosome; Differentiation; Lyase; KW Methylation; Nucleus; Phosphoprotein; Reference proteome; Repressor; KW Spermatogenesis; Transcription; Transcription regulation; Transferase. FT CHAIN 1..589 FT /note="Chromodomain Y-like protein" FT /id="PRO_0000292138" FT DOMAIN 55..115 FT /note="Chromo" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053" FT REGION 1..57 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 55..300 FT /note="Interaction with EZH2" FT /evidence="ECO:0000250|UniProtKB:Q9Y232" FT REGION 110..155 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 202..224 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 353..585 FT /note="Acetyl-CoA-binding domain" FT /evidence="ECO:0000255" FT COMPBIAS 15..29 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 30..54 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 118..142 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 205..219 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOD_RES 82 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:22673903" FT MOD_RES 129 FT /note="N6,N6,N6-trimethyllysine; by EHMT2; alternate" FT /evidence="ECO:0000250|UniProtKB:Q9Y232" FT MOD_RES 129 FT /note="N6,N6-dimethyllysine; by EHMT2; alternate" FT /evidence="ECO:0000250|UniProtKB:Q9Y232" FT MOD_RES 129 FT /note="N6-methyllysine; by EHMT2; alternate" FT /evidence="ECO:0000250|UniProtKB:Q9Y232" FT MOD_RES 164 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q9Y232" FT MOD_RES 195 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q9Y232" FT MOD_RES 210 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:22673903" FT VAR_SEQ 1..56 FT /note="MGLGSSQPSTKEAEPCTLQEKEEHPVDDTRQQNNAVPATVSDPDQVSPAVQD FT AETQ -> MASEELYE (in isoform 2)" FT /id="VSP_059157" SQ SEQUENCE 589 AA; 65031 MW; 6AE0CBAF89E30A21 CRC64; MGLGSSQPST KEAEPCTLQE KEEHPVDDTR QQNNAVPATV SDPDQVSPAV QDAETQVESI VDKRKNKKGK TEYLVRWKGY DSEDDTWEPE QHLVNCEEYI HDFNRRHNER QKEGTLARAN RASPSNARKQ ISRSTHSALS KTNPKALVVG KDHESKTNQL LATSQKFRKN TAPSLANRKN MDLAKSGIKI LVPKSPIKGR TSIDGFHGES PEKLDQGAED TVTPEVTAEK PTGALLGPGA ERARMGSRPR IHSLVPQVSG PVTAAMATTL AVNGKGTSPF MDALTANGTV TIQTSVTGVT AGKRKFIDDR RDQPFDKRLR FSVRQTESAY RYRDIVVRKQ DGFTHILLST KSSENNSLNP EVMKEVQSAL STAAADDSKL VLLSAVGSVF CCGLDFIYFI RRLTDDRKRE STKMAEAIRN FVNTFIQFKK PIIVAVNGPA IGLGASILPL CDVVWANEKA WFQTPYTTFG QSPDGCSTVM FPKIMGGASA NEMLLSGRKL TAQEACGKGL VSQVFWPGTF TQEVMVRIKE LASCNPIVLE ESKALVRCNM KMELEQANER ECDALKKIWG SAQGMDSMLK YLQRKIDEF //