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CDYL chromodomain Y like [ Homo sapiens (human) ]

Gene ID: 9425, updated on 5-Mar-2024

Summary

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Official Symbol
CDYLprovided by HGNC
Official Full Name
chromodomain Y likeprovided by HGNC
Primary source
HGNC:HGNC:1811
See related
Ensembl:ENSG00000153046 MIM:603778; AllianceGenome:HGNC:1811
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CDYL1
Summary
Chromodomain Y is a primate-specific Y-chromosomal gene family expressed exclusively in the testis and implicated in infertility. Although the Y-linked genes are testis-specific, this autosomal gene is ubiquitously expressed. The Y-linked genes arose by retrotransposition of an mRNA from this gene, followed by amplification of the retroposed gene. Proteins encoded by this gene superfamily possess a chromodomain, a motif implicated in chromatin binding and gene suppression, and a catalytic domain believed to be involved in histone acetylation. Multiple proteins are encoded by transcript variants of this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in placenta (RPKM 8.5), endometrium (RPKM 8.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6p25.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (4706138..4955544)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (4575080..4824553)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (4706372..4955778)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901549 Neighboring gene Sharpr-MPRA regulatory region 6592 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:4655389-4655960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4655961-4656532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4660676-4661494 Neighboring gene Sharpr-MPRA regulatory region 4929 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4694403-4694656 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:4719503-4720314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4725821-4726368 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4732250-4733140 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4733141-4734030 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4735211-4735409 Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 11 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:4772853-4773404 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4775329-4775982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16862 Neighboring gene NANOG hESC enhancer GRCh37_chr6:4787179-4787707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4788958-4789502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23897 Neighboring gene CDYL antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:4864691-4865890 Neighboring gene uncharacterized LOC105374897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4903364-4903864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16863 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4922310-4922536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4922523-4923034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4923035-4923546 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4925615-4926383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4924846-4925614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4932371-4933089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4947173-4947916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4971812-4972338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4972339-4972863 Neighboring gene MPRA-validated peak5629 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16865 Neighboring gene ribosomal protein S18 pseudogene 8 Neighboring gene LYRM4 antisense RNA 1 Neighboring gene ribonuclease P/MRP subunit p40

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy. Schoeler NE, et al. Epilepsia, 2018 Aug. PMID 30009487, Free PMC Article
  2. CDYL1 fosters double-strand break-induced transcription silencing and promotes homology-directed repair. Abu-Zhayia ER, et al. J Mol Cell Biol, 2018 Aug 1. PMID 29177481
  3. Chromodomain protein CDYL is required for transmission/restoration of repressive histone marks. Liu Y, et al. J Mol Cell Biol, 2017 Jun 1. PMID 28402439
  4. circCDYL/microRNA-105-5p participates in modulating growth and migration of colon cancer cells. Cui W, et al. Gen Physiol Biophys, 2019 Nov. PMID 31829306
  5. CDYL promotes the chemoresistance of small cell lung cancer by regulating H3K27 trimethylation at the CDKN1C promoter. Qiu Z, et al. Theranostics, 2019. PMID 31367252, Free PMC Article

See all (56) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Emerging functions and significance of circCDYL in human disorders.
    Title: Emerging functions and significance of circCDYL in human disorders.
  2. Hypoxia-induced circ-CDYL-EEF1A2 transcriptional complex drives lung metastasis of cancer stem cells from hepatocellular carcinoma.
    Title: Hypoxia-induced circ-CDYL-EEF1A2 transcriptional complex drives lung metastasis of cancer stem cells from hepatocellular carcinoma.
  3. circCDYL Acts as a Tumor Suppressor in Triple Negative Breast Cancer by Sponging miR-190a-3p and Upregulating TP53INP1.
    Title: circCDYL Acts as a Tumor Suppressor in Triple Negative Breast Cancer by Sponging miR-190a-3p and Upregulating TP53INP1.
  4. CDYL promotes the chemoresistance of small cell lung cancer by regulating H3K27 trimethylation at the CDKN1C promoter.
    Title: CDYL promotes the chemoresistance of small cell lung cancer by regulating H3K27 trimethylation at the CDKN1C promoter.
  5. circCDYL overexpression repressed cellular growth and migration via repressing miR-150-5p in colon cancer cells
    Title: circCDYL/microRNA-105-5p participates in modulating growth and migration of colon cancer cells.
  6. CDYL1 promotes the recruitment of enhancer of zeste homolog 2 (EZH2), stimulates local increase of the repressive methyl mark H3K27me3, and promotes transcription silencing at double-strand break sites.
    Title: CDYL1 fosters double-strand break-induced transcription silencing and promotes homology-directed repair.
  7. This study demonstrated that CDYL is the most likely candidate gene for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy.
    Title: Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy.
  8. CDYL plays an important role in the maintenance of repressive histone marks during replication, providing a mechanism for understanding of the epigenetic inheritance and memory.
    Title: Chromodomain protein CDYL is required for transmission/restoration of repressive histone marks.
  9. CDYL negatively regulates histone crotonylation by acting as a crotonyl-CoA hydratase to convert crotonyl-CoA to beta-hydroxybutyryl-CoA and suggest role in spermatogenesis.
    Title: Chromodomain Protein CDYL Acts as a Crotonyl-CoA Hydratase to Regulate Histone Crotonylation and Spermatogenesis.
  10. The epigenetic regulators CDYL and EZH2 to dendrite morphogenesis and might shed new light on our understanding of the regulation of the neurodevelopment.
    Title: Coordinated regulation of dendrite arborization by epigenetic factors CDYL and EZH2.
Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of smoking behaviours in patients with COPD.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC131936, DKFZp586C1622

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables crotonyl-CoA hydratase activity IDA
Inferred from Direct Assay
more info
 PubMed 
NOT enables methylated histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables methylated histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-macromolecule adaptor activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription corepressor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of peptidyl-lysine crotonylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in random inactivation of X chromosome ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatid development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatogenesis TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in chromosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
chromodomain Y-like protein
Names
CDY-like, autosomal
chromodomain protein, Y-like
crotonyl-CoA hydratase
testis-specific chromodomain Y-like protein
NP_001137442.1
NP_001137443.1
NP_001355054.1
NP_001355055.1
NP_001355056.1
NP_004815.3
XP_047275519.1
XP_047275520.1
XP_054212800.1
XP_054212801.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001143970.2 → NP_001137442.1  chromodomain Y-like protein isoform d

    See identical proteins and their annotated locations for NP_001137442.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter N-terminus compared to isoform a. Variants 4 and 5 both encode isoform d.
    Source sequence(s)
    AK296985, BC043397, BE874176
    Consensus CDS
    CCDS47364.1
    UniProtKB/Swiss-Prot
    Q9Y232
    Related
    ENSP00000394076.2, ENST00000449732.6
    Conserved Domains (1) summary
    cd06558
    Location:158 → 354
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  2. NM_001143971.2 → NP_001137443.1  chromodomain Y-like protein isoform d

    See identical proteins and their annotated locations for NP_001137443.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter N-terminus compared to isoform a. Variants 4 and 5 both encode isoform d.
    Source sequence(s)
    AF081258, BC043397, BE874176
    Consensus CDS
    CCDS47364.1
    UniProtKB/Swiss-Prot
    Q9Y232
    Related
    ENSP00000340908.5, ENST00000343762.5
    Conserved Domains (1) summary
    cd06558
    Location:158 → 354
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  3. NM_001368125.1 → NP_001355054.1  chromodomain Y-like protein isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) is predicted to encode the longest isoform (e). However, the presence of an upstream ORF may interfere with translation of the longest ORF. Translation of the upstream ORF would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL022725, AL356747, AL359643
    Consensus CDS
    CCDS93853.1
    UniProtKB/Swiss-Prot
    A8K6D6, B4DLG4, Q0VDG7, Q32NC5, Q5VX99, Q6P7T5, Q9BWZ2, Q9Y232, Q9Y424
    Related
    ENSP00000330512.5, ENST00000328908.9

  4. NM_001368126.1 → NP_001355055.1  chromodomain Y-like protein isoform f

    Status: REVIEWED

    Source sequence(s)
    AL022725, AL359643
    Conserved Domains (2) summary
    cd06558
    Location:268 → 464
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
    cd18634
    Location:6 → 57
    CD_CDY; chromodomain of the Chromodomain Y-like protein family

  5. NM_001368127.1 → NP_001355056.1  chromodomain Y-like protein isoform g

    Status: REVIEWED

    Source sequence(s)
    AL022725, AL359643
    Conserved Domains (1) summary
    cd06558
    Location:55 → 251
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  6. NM_004824.4 → NP_004815.3  chromodomain Y-like protein isoform a

    See identical proteins and their annotated locations for NP_004815.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AL022725, BC043397, BC108725, BE874176
    Consensus CDS
    CCDS4491.2
    UniProtKB/Swiss-Prot
    Q9Y232
    Related
    ENSP00000380718.3, ENST00000397588.8
    Conserved Domains (2) summary
    cd06558
    Location:290 → 486
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
    cd18634
    Location:6 → 57
    CD_CDY; chromodomain of the Chromodomain Y-like protein family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    4706138..4955544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419563.1 → XP_047275519.1  chromodomain Y-like protein isoform X1

  2. XM_047419564.1 → XP_047275520.1  chromodomain Y-like protein isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    4575080..4824553
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356825.1 → XP_054212800.1  chromodomain Y-like protein isoform X1

  2. XM_054356826.1 → XP_054212801.1  chromodomain Y-like protein isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_170752.1: Suppressed sequence

    Description
    NM_170752.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y232.2 GenPept UniProtKB/Swiss-Prot:Q9Y232

Gene LinkOut

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