tdp-1 Tar DNA-binding protein homolog 1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: tdp-1
Official Full Name: Tar DNA-binding protein homolog 1
Primary source: WormBase:WBGene00006514
Locus tag: CELE_F44G4.4
See related: AllianceGenome:WB:WBGene00006514
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 chromatin binding activity and single-stranded RNA binding activity. Involved in several processes, including RNA splicing; determination of adult lifespan; and hyperosmotic response. Located in nucleus. Is expressed in several structures, including body wall musculature; intestine; muscle cell; neurons; and pharynx. Used to study amyotrophic lateral sclerosis and amyotrophic lateral sclerosis type 10. Human ortholog(s) of this gene implicated in Parkinson's disease; amyotrophic lateral sclerosis; amyotrophic lateral sclerosis type 10; and motor neuron disease. Orthologous to human TARDBP (TAR DNA binding protein). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See tdp-1 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 7

Sequence:: Chromosome: II; NC_003280.10 (8997825..8999725)

Chromosome II - NC_003280.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

As nuclear RNAi involves chromatin changes moderated by HPL-2, a homolog of heterochromatin protein 1 (HP1), we investigated the interaction of TDP-1 and HPL-2. We found that TDP-1 and HPL-2 interact directly and that loss of TDP-1 dramatically alters the chromatin association of HPL-2.
Title: The Caenorhabditis elegans Ortholog of TDP-43 Regulates the Chromatin Localization of the Heterochromatin Protein 1 Homolog HPL-2.
TDP-1 regulates lifespan and proteotoxicity through DAF-16.
Title: RNA-processing protein TDP-43 regulates FOXO-dependent protein quality control in stress response.
These data show that the primary function of TDP-1, an ortholog of the neurodegeneration-associated RNA-binding protein TDP-43, is to limit formation or stability of double-stranded RNA.
Title: TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA.
It causes age-dependent toxicity to motor neurons.
Title: Evaluation of longevity enhancing compounds against transactive response DNA-binding protein-43 neuronal toxicity.
These results suggest that chronic induction of wild-type TDP-1/TDP-43 by cellular stress may propagate neurodegeneration and decrease lifespan.
Title: TDP-1/TDP-43 regulates stress signaling and age-dependent proteotoxicity in Caenorhabditis elegans.

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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

F44G4.4 (e-PCR)
- UniSTS:306318

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in RNA splicing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of adult lifespan	IGI Inferred from Genetic Interaction more info	PubMed
involved_in determination of adult lifespan	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hyperosmotic response	IEP Inferred from Expression Pattern more info	PubMed
involved_in hyperosmotic response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to oxidative stress	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to oxidative stress	IGI Inferred from Genetic Interaction more info	PubMed
involved_in response to oxidative stress	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	IEA Inferred from Electronic Annotation more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	HDA more info	PubMed
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: Tar DNA-binding protein homolog 1

NP_001022166.1

Confirmed by transcript evidence

NP_001254189.1

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_003280.10 Reference assembly

Range

8997825..8999725

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001267260.3 → NP_001254189.1 Tar DNA-binding protein homolog 1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001254189.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D0VWM8, Q20414, Q6BEV0

Conserved Domains (1) summary

cl17169
Location:174 → 247

RRM_SF; RNA recognition motif (RRM) superfamily
NM_001026995.8 → NP_001022166.1 Tar DNA-binding protein homolog 1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022166.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D0VWM8

Conserved Domains (1) summary

cl17169
Location:174 → 247

RRM_SF; RNA recognition motif (RRM) superfamily