KDM4D lysine demethylase 4D [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM4Dprovided by HGNC
Official Full Name: lysine demethylase 4Dprovided by HGNC
Primary source: HGNC:HGNC:25498
See related: Ensembl:ENSG00000186280 MIM:609766; AllianceGenome:HGNC:25498
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: JMJD2D
Summary: Enables histone H3K9me2/H3K9me3 demethylase activity. Involved in inflammatory response. Acts upstream of or within several processes, including cellular response to ionizing radiation; double-strand break repair via homologous recombination; and positive regulation of double-strand break repair via nonhomologous end joining. Located in site of double-strand break. Biomarker of nephroblastoma. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in testis (RPKM 26.3) and brain (RPKM 0.6) See more
Orthologs: mouse all
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Genomic context

Location:: 11q21

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (94973709..94999519)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (94980727..95006531)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (94706873..94732683)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MicroRNA-409-5p Inhibits GIST Tumorigenesis and Improves Imatinib Resistance by Targeting KDM4D Expression.
Title: MicroRNA-409-5p Inhibits GIST Tumorigenesis and Improves Imatinib Resistance by Targeting KDM4D Expression.
KDM4D enhances osteo/dentinogenic differentiation and migration of SCAPs via binding to RPS5.
Title: KDM4D enhances osteo/dentinogenic differentiation and migration of SCAPs via binding to RPS5.
Histone demethylase JMJD2D promotes the self-renewal of liver cancer stem-like cells by enhancing EpCAM and Sox9 expression.
Title: Histone demethylase JMJD2D promotes the self-renewal of liver cancer stem-like cells by enhancing EpCAM and Sox9 expression.
Demethylase-independent function of JMJD2D as a novel antagonist of p53 to promote Liver Cancer initiation and progression.
Title: Demethylase-independent function of JMJD2D as a novel antagonist of p53 to promote Liver Cancer initiation and progression.
Histone demethylase JMJD2D activates HIF1 signaling pathway via multiple mechanisms to promote colorectal cancer glycolysis and progression.
Title: Histone demethylase JMJD2D activates HIF1 signaling pathway via multiple mechanisms to promote colorectal cancer glycolysis and progression.
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.
KDM4D facilitates TLR4 transcription through demethylation of H3K9, thus activating TLR4/NF-kappaB signaling pathways in hepatic stellate cells, contributing to HSC activation and collagen crosslinking, further, hepatic fibrosis progression.
Title: The histone demethylase KDM4D promotes hepatic fibrogenesis by modulating Toll-like receptor 4 signaling pathway.
Results demonstrate that KDM4D mRNA and protein levels are upregulated in gastrointestinal stromal tumour (GIST). Its overexpression strongly promotes GIST cell proliferation, migration, invasion and angiogenesis. In contrast, its silencing reduced cell proliferation, migration, invasion and tumor angiogenesis. More importantly, these effects mediated by KDM4D might be dependent on the Hif1beta/VEGFA signaling pathway.
Title: Histone demethylase KDM4D promotes gastrointestinal stromal tumor progression through HIF1β/VEGFA signalling.
A high nuclear expression of KDM4D in samples of pancreatic resection margins significantly and independently predicted an earlier recurrence and could thus be used in the assessment of risk of relapse in clinical practice.
Title: KDM4D Predicts Recurrence in Exocrine Pancreatic Cells of Resection Margins from Patients with Pancreatic Adenocarcinoma.
The results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of preinitiation complex.
Title: H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication.

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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
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of lysine (K)-specific demethylase 4D (KDM4D) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin DNA binding	IEA Inferred from Electronic Annotation more info
enables damaged DNA binding	IEA Inferred from Electronic Annotation more info
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 H3K9me2/H3K9me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone demethylase activity	TAS Traceable Author Statement more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cellular response to ionizing radiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within double-strand break repair via homologous recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inflammatory response	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of chromatin binding	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of double-strand break repair via nonhomologous end joining	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in blood microparticle	HDA more info	PubMed
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IC Inferred by Curator more info	PubMed
located_in pericentric heterochromatin	IEA Inferred from Electronic Annotation more info
located_in site of double-strand break	IDA Inferred from Direct Assay 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; lysine (K)-specific demethylase 4D

NP_060509.2

EC 1.14.11.66

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.