DCL4 dicer-like 4 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: DCL4
Official Full Name: dicer-like 4
Primary source: TAIR:AT5G20320
Locus tag: AT5G20320
See related: Araport:AT5G20320
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: ATDCL4; dicer-like 4; DICER-LIKE 4; F5O24.210; F5O24_210
Summary: Encodes an RNase III-like enzyme that catalyzes processing of trans-acting small interfering RNA precursors in a distinct small RNA biogenesis pathway. The protein is also involved in the production of 21-nt primary siRNAs from both inverted-repeat constructs and endogenous sequences, as well as the RDR6-dependent 21-nt secondary siRNAs involved in long-range cell-to-cell signaling. It binds DRB4, a ds-RNA binding protein.
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Genomic context

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See DCL4 in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 25

Sequence:: Chromosome: 5; NC_003076.8 (6859212..6869307, complement)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The dicing activity of DCL3 and DCL4 is negatively affected by flavonoids.
Title: The dicing activity of DCL3 and DCL4 is negatively affected by flavonoids.
Biochemical characterization of the dicing activity of Dicer-like 2 in the model filamentous fungus Neurospora crassa.
Title: Biochemical characterization of the dicing activity of Dicer-like 2 in the model filamentous fungus Neurospora crassa.
Long DCL4-substrate dsRNAs efficiently induce RNA interference in plant cells.
Title: Long DCL4-substrate dsRNAs efficiently induce RNA interference in plant cells.
Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism.
Title: Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism.
characterization of missense alleles provides insights into its ability to process distinct classes of dsRNA substrates
Title: Characterization of DCL4 missense alleles provides insights into its ability to process distinct classes of dsRNA substrates.
DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation
Title: DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation.
results suggest that the spatial orientation of the Connector helix, Platform and PAZ relative to the RNase III domains is crucial for measuring dsRNA of defined length
Title: Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA.
Data demonstrate that different nutrient statuses of a host plant affect the post-translational regulation of the dicing activity of DCL3 and DCL4. Phosphate deficiency inhibited DCL3, and the activity of DCL3 was directly activated by inorganic phosphate.
Title: Post-Translational Regulation of the Dicing Activities of Arabidopsis DICER-LIKE 3 and 4 by Inorganic Phosphate and the Redox State.
CMA33/XCT modulates small RNA production through regulating the transcription of Dicer-Like Genes.
Title: CMA33/XCT Regulates Small RNA Production through Modulating the Transcription of Dicer-Like Genes in Arabidopsis.
DCL2/4-dependent and -independent RNA silencing pathways are involved, and may crosstalk with basal innate immunity pathways, in host defense and in cross-protection.
Title: Genetic analyses of the FRNK motif function of Turnip mosaic virus uncover multiple and potentially interactive pathways of cross-protection.

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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

NM_001203419.2

Supported by ESTs:

NM_001343652.1

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribonuclease III activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-templated transcription termination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within RNAi-mediated antiviral immune response	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within RNAi-mediated antiviral immunity against RNA virus	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within defense response to virus	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within defense response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lsiRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in miRNA processing	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ta-siRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vegetative phase change	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	HDA more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: dicer-like 4

NP_001190348.1

dicer-like 4 (DCL4); CONTAINS InterPro DOMAIN/s: Restriction endonuclease, type I, R subunit/Type III, Res subunit (InterPro:IPR006935), Double-stranded RNA-binding (InterPro:IPR001159), Argonaute/Dicer protein, PAZ (InterPro:IPR003100), Ribonuclease III (InterPro:IPR000999), Double-stranded RNA-binding-like (InterPro:IPR014720), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Dicer double-stranded RNA-binding fold (InterPro:IPR005034), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: dicer-like 2 (TAIR:AT3G03300.3).

NP_197532.3

dicer-like 4 (DCL4); CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), Double-stranded RNA-binding (InterPro:IPR001159), Argonaute/Dicer protein, PAZ (InterPro:IPR003100), Ribonuclease III (InterPro:IPR000999), Double-stranded RNA-binding-like (InterPro:IPR014720), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Dicer double-stranded RNA-binding fold (InterPro:IPR005034), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: dicer-like 2 (TAIR:AT3G03300.3); Has 20138 Blast hits to 15531 proteins in 2958 species: Archae - 325; Bacteria - 10957; Metazoa - 2671; Fungi - 1592; Plants - 1161; Viruses - 33; Other Eukaryotes - 3399 (source: NCBI BLink).

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_003076.8 Reference assembly

Range

6859212..6869307 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_122039.5 → NP_197532.3 dicer-like 4 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_197532.3

Status: REVIEWED

UniProtKB/Swiss-Prot

P84634, Q3SA53

UniProtKB/TrEMBL

A0A654G3G2

Conserved Domains (9) summary

smart00949
Location:937 → 1080

PAZ; This domain is named PAZ after the proteins Piwi Argonaut and Zwille

smart00358
Location:1463 → 1527

DSRM; Double-stranded RNA binding motif

COG0571
Location:1285 → 1531

Rnc; dsRNA-specific ribonuclease [Transcription]

COG1111
Location:124 → 640

MPH1; ERCC4-related helicase [Replication, recombination and repair]

cd00046
Location:138 → 289

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:1621 → 1681

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:1308 → 1452

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 ...

pfam00271
Location:470 → 589

Helicase_C; Helicase conserved C-terminal domain

pfam03368
Location:657 → 740

Dicer_dimer; Dicer dimerization domain
NM_001203419.2 → NP_001190348.1 dicer-like 4 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001190348.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A654G3G2, F4K482

Conserved Domains (9) summary

smart00949
Location:923 → 1066

PAZ; This domain is named PAZ after the proteins Piwi Argonaut and Zwille

smart00358
Location:1449 → 1513

DSRM; Double-stranded RNA binding motif

COG0571
Location:1271 → 1517

Rnc; dsRNA-specific ribonuclease [Transcription]

COG1111
Location:124 → 626

MPH1; ERCC4-related helicase [Replication, recombination and repair]

cd00046
Location:138 → 275

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:1607 → 1667

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:1294 → 1438

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 ...

pfam00271
Location:456 → 575

Helicase_C; Helicase conserved C-terminal domain

pfam03368
Location:643 → 726

Dicer_dimer; Dicer dimerization domain
NM_001343652.1 → NP_001330078.1 dicer-like 4 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B9N9, A0A7G2F8Y9