rbr-2 Lysine-specific demethylase rbr-2;[histone H3]-trimethyl-L-lysine(4) demethylase [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: rbr-2
Official Full Name: Lysine-specific demethylase rbr-2;[histone H3]-trimethyl-L-lysine(4) demethylase
Primary source: WormBase:WBGene00004319
Locus tag: CELE_ZK593.4
See related: AllianceGenome:WB:WBGene00004319
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity. Involved in determination of adult lifespan and regulation of vulval development. Located in nucleus. Is expressed widely. 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, Dec 2024]
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Genomic context

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See rbr-2 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 10

Sequence:: Chromosome: IV; NC_003282.8 (10920070..10926817)

Chromosome IV - NC_003282.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003282.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RBR-2 did not play a comparable role in the maintenance of quiescent germ cells in dauer larvae, implying that it represses stress that occurs as a consequence of germ cell proliferation, rather than stress that accumulates in nondividing cells.
Title: H3K4 demethylase activities repress proliferative and postmitotic aging.
there is a link between RBR-2 activity, H3K4me3 levels, the NURF complex and the expression of WSP-1
Title: The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1.
RBR-2 is not involved in preventing H3K4me3 deposition in the P lineage, but could play a role in regulating somatic deposition of H3K4me3.
Title: Lineage specific trimethylation of H3 on lysine 4 during C. elegans early embryogenesis.
findings show that mutation or RNAi depletion of rbr-2 leads to increased levels of trimethylated histone 3 lysine 4 during larval development and defects in vulva formation
Title: RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ZK593.4 (e-PCR)
- UniSTS:308283

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables 2-oxoglutarate-dependent dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone modifying activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
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 determination of adult lifespan	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 DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of vulval development	IMP Inferred from Mutant Phenotype 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 nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Lysine-specific demethylase rbr-2;[histone H3]-trimethyl-L-lysine(4) demethylase

NP_001293922.1

Confirmed by transcript evidence

NP_502032.2

Confirmed by transcript evidence

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_003282.8 Reference assembly

Range

10920070..10926817

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_069631.7 → NP_502032.2 Lysine-specific demethylase rbr-2 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_502032.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q23541

Conserved Domains (8) summary

smart00501
Location:122 → 214

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00545
Location:55 → 96

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

pfam02373
Location:501 → 617

JmjC; JmjC domain, hydroxylase

smart00249
Location:1208 → 1254

PHD; PHD zinc finger

cd15610
Location:1413 → 1463

PHD3_KDM5A_like; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins

pfam02928
Location:709 → 761

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:788 → 1130

PLU-1; PLU-1-like protein

cl22851
Location:321 → 368

PHD_SF; PHD finger superfamily
NM_001306993.3 → NP_001293922.1 [histone H3]-trimethyl-L-lysine(4) demethylase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001293922.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A061ACP3

Conserved Domains (8) summary

smart00501
Location:89 → 181

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00545
Location:22 → 63

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

pfam02373
Location:468 → 584

JmjC; JmjC domain, hydroxylase

smart00249
Location:1175 → 1221

PHD; PHD zinc finger

cd15610
Location:1380 → 1430

PHD3_KDM5A_like; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins

pfam02928
Location:676 → 728

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:755 → 1097

PLU-1; PLU-1-like protein

cl22851
Location:288 → 335

PHD_SF; PHD finger superfamily