JHD2 histone demethylase [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: JHD2
Official Full Name: histone demethylase
Primary source: SGD:S000003880
Locus tag: YJR119C
See related: AllianceGenome:SGD:S000003880; FungiDB:YJR119C; VEuPathDB:YJR119C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: KDM5
Summary: Enables histone H3K4 demethylase activity. Involved in several processes, including antisense RNA transcript catabolic process; regulation of chromosome condensation; and regulation of gene expression. Located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in ankylosing spondylitis; breast cancer; descending colon cancer; high grade glioma; and intellectual disability (multiple). Orthologous to several human genes including KDM5A (lysine demethylase 5A); KDM5B (lysine demethylase 5B); and KDM5C (lysine demethylase 5C). [provided by Alliance of Genome Resources, Oct 2024]
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Genomic context

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See JHD2 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 1

Sequence:: Chromosome: X; NC_001142.9 (644304..646490, complement)

Chromosome X - NC_001142.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001142.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A model has been proposed wherein combined actions of Set1 and Jhd2 via modulating H3K4 methylation-demethylation together control chromatin dynamics during various facets of transcriptional regulation.
Title: Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription.
H2B Lys-123 ubiquitination blocks Jhd2 from accessing its binding site on chromatin, and thereby, we have uncovered a second mechanism by which H2B ubiquitination contributes to the trans-histone regulation of H3K4 methylation.
Title: Interaction of the Jhd2 Histone H3 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination.
Jhd2, an evolutionarily conserved JARID1 family H3 Lys4 demethylase, effects all states of methylated histone H3K4 within the NTS regions of rDNA, and its activity is required for the regulation of rDNA silencing in a Sir2-independent manner.
Title: Yeast histone H3 lysine 4 demethylase Jhd2 regulates mitotic rDNA condensation.
the JmjN domain of Jhd2 is important for its protein stability, and the plant homeodomain (PHD) finger mediates its chromatin association independent of H3K4 methylation
Title: The JmjN domain of Jhd2 is important for its protein stability, and the plant homeodomain (PHD) finger mediates its chromatin association independent of H3K4 methylation.
the protein level of the yeast histone H3 Lys 4 (H3 K4) demethylase Jhd2/Kdm5 is modulated through polyubiquitination by the E3 ubiquitin ligase Not4 and turnover by the proteasome
Title: Polyubiquitination of the demethylase Jhd2 controls histone methylation and gene expression.
Ectopic overexpression of mouse Jarid1B, a Yjr119Cp homolog, greatly diminished H3-(lysine) K4me3 and H3-K4me2 in HeLa cells, suggesting these proteins function as K4 demethylases in vivo.
Title: Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins.
A novel budding yeast JmjC domain-containing H3-K4 demethylase, Jhd2p, that antagonizes the trimethyl modification state and contributes to regulation of telomeric silencing.
Title: Yeast Jhd2p is a histone H3 Lys4 trimethyl 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

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in antisense RNA transcript catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic cell cycle process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rDNA heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of chromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of chromosome condensation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sporulation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	HDA more info	PubMed
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: histone demethylase

NP_012653.1

EC 1.14.11.67

JmjC domain family histone demethylase; promotes global demethylation of H3K4 and represses noncoding intergenic transcription during sporulation; removes methyl groups added by Set1p; phosphorylation by Tpk2p during glycolysis inhibits activity, nuclear localization, chromatin binding and promotes Not4p Ub-mediated degradation; negatively regulated by H3K14 acetylation; regulates sporulation timing by extending period of active transcription; regulates rDNA silencing; human homolog is JARID1C

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

NC_001142.9 Reference assembly

Range

644304..646490 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001181777.1 → NP_012653.1 TPA: histone demethylase [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_012653.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VWT8, P47156

UniProtKB/TrEMBL

C8ZBR7, G2WHC2, N1P096

Conserved Domains (4) summary

smart00545
Location:3 → 46

JmjN; Small domain found in the jumonji family of transcription factors

cd15544
Location:237 → 282

PHD_BAZ1A_like; PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B

pfam02373
Location:414 → 532

JmjC; JmjC domain, hydroxylase

cl02608
Location:260 → 320

BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...