Kdm4A Lysine demethylase 4A [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: Kdm4Aprovided by FlyBase
Official Full Name: Lysine demethylase 4Aprovided by FlyBase
Primary source: FLYBASE:FBgn0033233
Locus tag: Dmel_CG15835
See related: AllianceGenome:FB:FBgn0033233
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: CG15835; dJMJD2(1); dkdm4a; dKDM4A; Dmel\CG15835; JMJD2A; JMJD2AKDM4A; kdm4a; Kdm4a; KDM4A
Summary: Enables histone H3-methyl-lysine-36 demethylase activity and histone H3-methyl-lysine-9 demethylase activity. Involved in histone H3-K36 demethylation; histone H3-K9 demethylation; and positive regulation of gene expression. Located in heterochromatin and nucleus. Is expressed in anterior endoderm anlage; head mesoderm; organism; posterior endoderm; and trunk mesoderm. Human ortholog(s) of this gene implicated in several diseases, including autistic disorder; gastrointestinal system cancer (multiple); head and neck cancer; malignant peripheral nerve sheath tumor; and withdrawal disorder. Orthologous to several human genes including KDM4A (lysine demethylase 4A) and KDM4C (lysine demethylase 4C). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: 43F2-43F2; 2-57 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	2R	NT_033778.4 (7922775..7924988, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	2R	NT_033778.3 (3810280..3812493, complement)

Chromosome 2R - NT_033778.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the temporal kinetics and pathway utilization during heterochromatic DSB repair depend on dKDM4A-dependent demethylation of heterochromatic histone marks
Title: Timely double-strand break repair and pathway choice in pericentromeric heterochromatin depend on the histone demethylase dKDM4A.
dKDM4A, in addition to its previously characterized role in euchromatin, utilizes both enzymatic and structural mechanisms to regulate heterochromatin organization and functions.
Title: Drosophila Histone Demethylase KDM4A Has Enzymatic and Non-enzymatic Roles in Controlling Heterochromatin Integrity.
Jra recruits the HP1a/KDM4A complex to its gene body region upon osmotic stress to reduce H3K36 methylation levels and disrupt H3K36 methylation-dependent histone deacetylation
Title: HP1a/KDM4A is involved in the autoregulatory loop of the oncogene gene c-Jun.
Appropriate expression levels for some dKDM4A-regulated genes rely on the demethylase activity of dKDM4A, whereas others do not.
Title: Gene regulation by the lysine demethylase KDM4A in Drosophila.
binding to HP1a is required for dKDM4A-mediated H3K36me3 demethylation at a subset of heterochromatic genes. Collectively, these results show that HP1a functions to target the H3K36 demethylase dKDM4A to heterochromatic genes in Drosophila
Title: HP1a targets the Drosophila KDM4A demethylase to a subset of heterochromatic genes to regulate H3K36me3 levels.
these results have implications for the role of the epigenetic regulator Dmel\Kdm4A in the control of genes involved in life span and male-specific sex determination in the fly.
Title: The histone demethylase Dmel\Kdm4A controls genes required for life span and male-specific sex determination in Drosophila.
These results suggest a function of HP1a in transcription facilitating H3K36 demethylation at transcribed and/or heterochromatin regions by dKDM4A (CG15835).
Title: Heterochromatin protein 1a stimulates histone H3 lysine 36 demethylation by the Drosophila KDM4A demethylase.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables histone H3K36 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K36me2/H3K36me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K36me2/H3K36me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K56me2/H3K56me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9me2/H3K9me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
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 nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: lysine demethylase 4A

Names: CG15835-PA; CG15835-PB; Kdm4A-PA; Kdm4A-PB; histone demethylase 4A; lysine (K)-specific demethylase 4A

NP_001246194.1

EC 1.14.11.66

EC 1.14.11.69

NP_610331.1

EC 1.14.11.66

EC 1.14.11.69

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NT_033778.4 Reference assembly

Range

7922775..7924988 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001259265.2 → NP_001246194.1 lysine demethylase 4A, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001246194.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A0B4K7U3

Conserved Domains (2) summary

pfam02373
Location:182 → 298

JmjC; JmjC domain, hydroxylase

cl15840
Location:17 → 59

JmjN; jmjN domain
NM_136487.4 → NP_610331.1 lysine demethylase 4A, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_610331.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9V333

Related

FBpp0087961

Conserved Domains (2) summary

pfam02373
Location:182 → 298

JmjC; JmjC domain, hydroxylase

cl15840
Location:17 → 59

JmjN; jmjN domain