dcr-1 Death-promoting deoxyribonuclease [Caenorhabditis elegans] - Gene

Summary

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Gene symbol: dcr-1
Gene description: Death-promoting deoxyribonuclease
Primary source: WormBase:WBGene00000939
Locus tag: CELE_K12H4.8
See related: AllianceGenome:WB:WBGene00000939
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 deoxyribonuclease I activity and ribonuclease III activity. Involved in several processes, including nucleic acid metabolic process; olfactory learning; and positive regulation of primary miRNA processing. Acts upstream of or within defense response to Gram-positive bacterium. Located in cytosol and nucleus. Is expressed in germ line; intestine; neurons; and somatic cell. Human ortholog(s) of this gene implicated in colorectal cancer; hepatocellular carcinoma; multinodular goiter; nephroma; and pleuropulmonary blastoma. Orthologous to human DICER1 (dicer 1, ribonuclease III). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: III

Exon count:: 27

Sequence:: Chromosome: III; NC_003281.10 (8071967..8080281, complement)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

role for pash-1 in miRNA maturation and miRNA-mediated gene regulation.
Title: Processing of primary microRNAs by the Microprocessor complex.
Report of transcriptome-wide map of Dicer targets; identify thousands of Dicer-binding sites in human cells and C. elegans; find known and hundreds of additional miRNAs; also report structural RNAs, promoter RNAs, and mitochondrial transcripts as Dicer targets; most Dicer-binding sites reside on mRNAs/lncRNAs and are not significantly processed into small RNAs.
Title: A variety of dicer substrates in human and C. elegans.
Cleavage of DCR-1 by caspase 3 may cause a conformational change that allows truncated DCR-1 to bind and process DNA, and may remove steric hindrance that blocks DNA access to truncated DCR-1.
Title: A novel mechanism underlies caspase-dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis.
[review] Dicer-1 lacks a functional helicase domain and is responsible for processing pre-microRNAs into mature miRNAs.
Title: Dicer's role as an antiviral: still an enigma.
Taken together, these results uncover a previously unknown role for DCR-1/Dicer in C. elegans antibacterial immunity that is largely associated with miRNA processing.
Title: New role for DCR-1/dicer in Caenorhabditis elegans innate immunity against the highly virulent bacterium Bacillus thuringiensis DB27.
Results show that the tandem tudor protein ERI-5 potentiates ERI endo-RNAi by tethering an RNA-dependent RNA polymerase (RdRP, F10B5.7) module to DCR-1.
Title: Tudor domain ERI-5 tethers an RNA-dependent RNA polymerase to DCR-1 to potentiate endo-RNAi.
Dicer's helicase domain discriminates dsRNA termini to promote an altered reaction mode
Title: Dicer's helicase domain discriminates dsRNA termini to promote an altered reaction mode.
the GLH-1/DCR-1 complex may function in the transport, deposition, or regulation of maternally-transcribed mRNAs and their associated miRNAs.
Title: C. elegans Dicer interacts with the P-granule component GLH-1 and both regulate germline RNPs.
the helicase domain of Dicer is not necessary for microRNA (miRNA) processing, or RNA interference following exposure to exogenous double-stranded RNA
Title: Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs.
findings show that DCR-1 functions in fragmenting chromosomal DNA during apoptosis, in addition to processing of small RNAs, and undergoes a protease-mediated conversion from a ribonuclease to a deoxyribonuclease
Title: Caspase-dependent conversion of Dicer ribonuclease into a death-promoting deoxyribonuclease.

Submit: New GeneRIF Correction See all GeneRIFs (12)

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

K12H4.8 (e-PCR)
- UniSTS:311940

K06H7.6 (e-PCR)
- UniSTS:311442

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA endonuclease activity, producing 5'-phosphomonoesters	IEA Inferred from Electronic Annotation more info
enables deoxyribonuclease I activity	IBA Inferred from Biological aspect of Ancestor more info
enables deoxyribonuclease I activity	IDA Inferred from Direct Assay more info	PubMed
enables endonuclease activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclease activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribonuclease III activity	IBA Inferred from Biological aspect of Ancestor more info
enables ribonuclease III activity	IDA Inferred from Direct Assay more info	PubMed
enables ribonuclease III activity	IEA Inferred from Electronic Annotation more info
enables ribonuclease III activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA processing	IEA Inferred from Electronic Annotation more info
involved_in apoptotic DNA fragmentation	IBA Inferred from Biological aspect of Ancestor more info
involved_in apoptotic DNA fragmentation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cellular component organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within defense response to Gram-positive bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gonad morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ncRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in nematode larval development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in olfactory learning	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of primary miRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pre-miRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in pre-miRNA processing	IEA Inferred from Electronic Annotation more info
involved_in pre-miRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of development, heterochronic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulatory ncRNA-mediated gene silencing	IEA Inferred from Electronic Annotation more info
involved_in reproductive process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in siRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in siRNA processing	IEA Inferred from Electronic Annotation more info
involved_in siRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of RISC-loading complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	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

General protein information

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Preferred Names: Death-promoting deoxyribonuclease

NP_498761.2

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_003281.10 Reference assembly

Range

8071967..8080281 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_066360.4 → NP_498761.2 Death-promoting deoxyribonuclease [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_498761.2

Status: REVIEWED

UniProtKB/Swiss-Prot

P34529

Conserved Domains (9) summary

smart00490
Location:434 → 498

HELICc; helicase superfamily c-terminal domain

smart00535
Location:1395 → 1520

RIBOc; Ribonuclease III family

COG0571
Location:1639 → 1900

Rnc; dsRNA-specific ribonuclease [Transcription]

cd00046
Location:27 → 183

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00048
Location:1834 → 1894

DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...

cd00593
Location:1659 → 1824

RIBOc; RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in ...

cd02843
Location:836 → 956

PAZ_dicer_like; PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named ...

cd15903
Location:248 → 343

Dicer_PBD; Partner-binding domain of the endoribonuclease Dicer

pfam03368
Location:572 → 659

Dicer_dimer; Dicer dimerization domain