CDYL_RAT
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 03-AUG-2022, entry version 126.
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}.
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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; Q6AYK9; -.
DR PRIDE; Q6AYK9; -.
DR Ensembl; ENSRNOT00000100703; ENSRNOP00000095115; ENSRNOG00000032215. [Q6AYK9-2]
DR GeneID; 361237; -.
DR KEGG; rno:361237; -.
DR UCSC; RGD:1549745; rat. [Q6AYK9-1]
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 OMA; VPRSPMN; -.
DR OrthoDB; 1471901at2759; -.
DR PhylomeDB; Q6AYK9; -.
DR TreeFam; TF313375; -.
DR PRO; PR:Q6AYK9; -.
DR Proteomes; UP000002494; Chromosome 17.
DR Bgee; ENSRNOG00000032215; Expressed in testis and 19 other tissues.
DR Genevisible; Q6AYK9; RN.
DR GO; GO:0005694; C:chromosome; ISS:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0016607; C:nuclear speck; IEA:Ensembl.
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 Gene3D; 1.10.12.10; -; 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 Pfam; PF00385; Chromo; 1.
DR Pfam; PF00378; ECH_1; 1.
DR SMART; SM00298; CHROMO; 1.
DR SUPFAM; SSF52096; SSF52096; 1.
DR SUPFAM; SSF54160; SSF54160; 1.
DR PROSITE; PS00598; CHROMO_1; 1.
DR PROSITE; PS50013; CHROMO_2; 1.
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
