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Kdm4d lysine (K)-specific demethylase 4D [ Mus musculus (house mouse) ]

Gene ID: 244694, updated on 2-Nov-2024

Summary

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Official Symbol
Kdm4dprovided by MGI
Official Full Name
lysine (K)-specific demethylase 4Dprovided by MGI
Primary source
MGI:MGI:3606484
See related
Ensembl:ENSMUSG00000053914 AllianceGenome:MGI:3606484
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Jmjd2d; 4932416A15
Summary
Enables chromatin DNA binding activity; damaged DNA binding activity; and histone H3K9 demethylase activity. Acts upstream of or within DNA damage response. Located in nucleus; pericentric heterochromatin; and site of double-strand break. Orthologous to human KDM4D (lysine demethylase 4D). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Restricted expression toward testis adult (RPKM 31.3) See more
Orthologs
human all
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Genomic context

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See Kdm4d in Genome Data Viewer
Location:
9 A1- A2; 9 4.05 cM
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (14373844..14411818, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (14462548..14500522, complement)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene endonuclease domain containing 1 Neighboring gene predicted gene, 34156 Neighboring gene STARR-seq mESC enhancer starr_23348 Neighboring gene lysine (K)-specific demethylase 4D-like Neighboring gene STARR-positive B cell enhancer ABC_E248 Neighboring gene CWC15 spliceosome-associated protein Neighboring gene angiomotin-like 1 Neighboring gene predicted gene, 34263

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Kdm4d mutant mice show impaired sperm motility and subfertility. Xu Z, et al. J Reprod Dev, 2024 Oct 1. PMID 39034148, Free PMC Article
  2. Embryonic development following somatic cell nuclear transfer impeded by persisting histone methylation. Matoba S, et al. Cell, 2014 Nov 6. PMID 25417163, Free PMC Article
  3. Demethylase JMJD2D induces PD-L1 expression to promote colorectal cancer immune escape by enhancing IFNGR1-STAT3-IRF1 signaling. Chen Q, et al. Oncogene, 2022 Mar. PMID 35027670
  4. Repressive histone methylation regulates cardiac myocyte cell cycle exit. El-Nachef D, et al. J Mol Cell Cardiol, 2018 Aug. PMID 29800554, Free PMC Article
  5. Histone Demethylase JMJD2D Interacts With β-Catenin to Induce Transcription and Activate Colorectal Cancer Cell Proliferation and Tumor Growth in Mice. Peng K, et al. Gastroenterology, 2019 Mar. PMID 30472235

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Kdm4d mutant mice show impaired sperm motility and subfertility.
    Title: Kdm4d mutant mice show impaired sperm motility and subfertility.
  2. Histone demethylase JMJD2D protects against enteric bacterial infection via up-regulating colonic IL-17F to induce beta-defensin expression.
    Title: Histone demethylase JMJD2D protects against enteric bacterial infection via up-regulating colonic IL-17F to induce β-defensin expression.
  3. Demethylase JMJD2D induces PD-L1 expression to promote colorectal cancer immune escape by enhancing IFNGR1-STAT3-IRF1 signaling.
    Title: Demethylase JMJD2D induces PD-L1 expression to promote colorectal cancer immune escape by enhancing IFNGR1-STAT3-IRF1 signaling.
  4. TRIM14 inhibits OPTN-mediated autophagic degradation of KDM4D to epigenetically regulate inflammation.
    Title: TRIM14 inhibits OPTN-mediated autophagic degradation of KDM4D to epigenetically regulate inflammation.
  5. Inflammation-induced JMJD2D promotes colitis recovery and colon tumorigenesis by activating Hedgehog signaling.
    Title: Inflammation-induced JMJD2D promotes colitis recovery and colon tumorigenesis by activating Hedgehog signaling.
  6. Histone demethylase KDM4D cooperates with NFIB and MLL1 complex to regulate adipogenic differentiation of C3H10T1/2 mesenchymal stem cells.
    Title: Histone demethylase KDM4D cooperates with NFIB and MLL1 complex to regulate adipogenic differentiation of C3H10T1/2 mesenchymal stem cells.
  7. To determine the epigenetic mechanisms limiting CM cycling in adult cardiac myocytes (CMs) (ACMs) and whether trimethylation of lysine 9 of histone H3 (H3K9me3), a histone modification associated with repressed chromatin, is required for the silencing of cell cycle genes, we developed a transgenic mouse model where H3K9me3 is specifically removed in CMs by overexpression of histone demethylase, KDM4D
    Title: Repressive histone methylation regulates cardiac myocyte cell cycle exit.
  8. JMJD2D interacts with b-catenin to activate transcription of its target genes and promote CRC cell proliferation, migration, and invasion, as well as formation of colorectal tumors in mice.
    Title: Histone Demethylase JMJD2D Interacts With β-Catenin to Induce Transcription and Activate Colorectal Cancer Cell Proliferation and Tumor Growth in Mice.
  9. These results suggest that demethylation of H3K9 in round spermatids is dispensable for spermatogenesis but that possible defects in Kdm4d-null elongating spermatids could be rescued by functional redundancy of the KDM4B demethylase.
    Title: The testis-enriched histone demethylase, KDM4D, regulates methylation of histone H3 lysine 9 during spermatogenesis in the mouse but is dispensable for fertility.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (2)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables chromatin DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables damaged DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K9 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K9 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H3K9 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K9me2/H3K9me3 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K9me2/H3K9me3 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within cellular response to ionizing radiation ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in inflammatory response ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within positive regulation of chromatin binding ISO
Inferred from Sequence Orthology
more info
 PubMed 
acts_upstream_of_or_within positive regulation of double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of protein phosphorylation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of protein phosphorylation ISO
Inferred from Sequence Orthology
more info
 PubMed 
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
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 
located_in pericentric heterochromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
 PubMed 

General protein information

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Preferred Names
lysine-specific demethylase 4D
Names
[histone H3]-trimethyl-L-lysine(9) demethylase 4D
jmjC domain-containing histone demethylation protein 3D
jumonji domain containing 2D
jumonji domain-containing protein 2D
NP_001397435.1
NP_775609.2
XP_006510333.1

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_001410506.1 → NP_001397435.1  lysine-specific demethylase 4D

    Status: VALIDATED

    Source sequence(s)
    CT485607
    UniProtKB/Swiss-Prot
    A2CGB5, B8JK34, Q2M1G7, Q3U2K5, Q8BI19
    Related
    ENSMUSP00000111311.3, ENSMUST00000115647.3

  2. NM_173433.3 → NP_775609.2  lysine-specific demethylase 4D

    See identical proteins and their annotated locations for NP_775609.2

    Status: VALIDATED

    Source sequence(s)
    CT485607
    Consensus CDS
    CCDS22822.2
    UniProtKB/Swiss-Prot
    A2CGB5, B8JK34, Q2M1G7, Q3U2K5, Q8BI19
    UniProtKB/TrEMBL
    Z4YLE9
    Related
    ENSMUSP00000061632.7, ENSMUST00000058796.7
    Conserved Domains (2) summary
    smart00545
    Location:15 → 55
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000075.7 Reference GRCm39 C57BL/6J

    Range
    14373844..14411818 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006510270.2 → XP_006510333.1  lysine-specific demethylase 4D isoform X1

    See identical proteins and their annotated locations for XP_006510333.1

    UniProtKB/Swiss-Prot
    A2CGB5, B8JK34, Q2M1G7, Q3U2K5, Q8BI19
    UniProtKB/TrEMBL
    Z4YLE9
    Conserved Domains (2) summary
    smart00545
    Location:15 → 55
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3U2K5.2 GenPept UniProtKB/Swiss-Prot:Q3U2K5

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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