DCL3 dicer-like 3 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Gene symbol: DCL3
Gene description: dicer-like 3
Primary source: Araport:AT3G43920
Locus tag: AT3G43920
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: ATDCL3; dicer-like 3; DICER-LIKE 3
Summary: Encodes a ribonuclease III family protein that is required for endogenous RDR2-dependent siRNA (but not miRNA) formation.
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Genomic context

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See DCL3 in Genome Data Viewer

Location:: chromosome: 3

Exon count:: 24

Sequence:: Chromosome: 3; NC_003074.8 (15753387..15760859)

Chromosome 3 - NC_003074.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003074.8

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.
A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation.
Title: A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation.
Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation.
Title: Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation.
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.
RDR2 converts Pol IV transcripts into double-stranded RNAs and then typically adds an extra untemplated 3' terminal nucleotide to the second strands. The dicer endonuclease DCL3 cuts resulting duplexes to generate 24- and 23-nt siRNAs.
Title: Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway.
DCL3 triplet repeat expansions can lead to local siRNA biogenesis, which in turn downregulates transcription through an RdDM-dependent epigenetic modification
Title: RNA-Dependent Epigenetic Silencing Directs Transcriptional Downregulation Caused by Intronic Repeat Expansions.
DDL is required for the optimal activity of DCL3.
Title: DAWDLE Interacts with DICER-LIKE Proteins to Mediate Small RNA Biogenesis.
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.
This expression-dependent RdDM mechanism functions through RNAi degradation of transposable element mRNAs into small RNAs guided by the RNA-dependent RNA polymerase 6 (RDR6) protein and is therefore referred to as RDR6-RdDM.We identified a new mechanism of expression-dependent RdDM, which functions through DICER-LIKE3 (DCL3) but bypasses the requirement of both RNA polymerase IV and RDR6 (termed DCL3-RdDM).
Title: Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation.
The authors identified Pol IV and RDR2-dependent RNAs (P4R2 RNAs) that accumulate in dcl3 mutants and are diced into 24 nt RNAs by DCL3 in vitro.
Title: Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis.

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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_001161190.2

Supported by ESTs:

NM_001161191.3

Supported by ESTs:

NM_001339116.1

Supported by ESTs:

NM_114260.1

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables double-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
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
involved_in RNA processing	IEA Inferred from Electronic Annotation more info
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
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 siRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ta-siRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	IDA Inferred from Direct Assay 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 3

NP_001154662.2

dicer-like 3 (DCL3); CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), DEAD-like helicase, N-terminal (InterPro:IPR014001), Argonaute/Dicer protein, PAZ (InterPro:IPR003100), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), Ribonuclease III (InterPro:IPR000999); BEST Arabidopsis thaliana protein match is: dicer-like 1 (TAIR:AT1G01040.1); Has 13510 Blast hits to 8657 proteins in 2649 species: Archae - 187; Bacteria - 7967; Metazoa - 1616; Fungi - 695; Plants - 614; Viruses - 37; Other Eukaryotes - 2394 (source: NCBI BLink).

NP_001154663.2

dicer-like 3 (DCL3); CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), DEAD-like helicase, N-terminal (InterPro:IPR014001), Argonaute/Dicer protein, PAZ (InterPro:IPR003100), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), Ribonuclease III (InterPro:IPR000999); BEST Arabidopsis thaliana protein match is: dicer-like 1 (TAIR:AT1G01040.1); Has 13599 Blast hits to 8740 proteins in 2670 species: Archae - 198; Bacteria - 7991; Metazoa - 1636; Fungi - 703; Plants - 621; Viruses - 45; Other Eukaryotes - 2405 (source: NCBI BLink).

NP_189978.1

dicer-like 3 (DCL3); CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), DEAD-like helicase, N-terminal (InterPro:IPR014001), Argonaute/Dicer protein, PAZ (InterPro:IPR003100), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), Ribonuclease III (InterPro:IPR000999); BEST Arabidopsis thaliana protein match is: dicer-like 4 (TAIR:AT5G20320.1); Has 13386 Blast hits to 8472 proteins in 2623 species: Archae - 174; Bacteria - 7922; Metazoa - 1543; Fungi - 728; Plants - 598; Viruses - 37; Other Eukaryotes - 2384 (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_003074.8 Reference assembly

Range

15753387..15760859

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001339114.1 → NP_001325812.1 dicer-like 3 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1I9LMD3, A0A5S9XHN9
NM_001339115.1 → NP_001325811.1 dicer-like 3 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1I9LMD2, A0A5S9XHN9
NM_001161191.3 → NP_001154663.2 dicer-like 3 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001154663.2

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9XHN9, F4J0I5

Conserved Domains (5) summary

COG0571
Location:1190 → 1425

Rnc; dsRNA-specific ribonuclease [Transcription]

cd00046
Location:58 → 203

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.

cd00593
Location:1204 → 1351

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 ...

cd02844
Location:814 → 952

PAZ_CAF_like; PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA ...

pfam00271
Location:382 → 496

Helicase_C; Helicase conserved C-terminal domain
NM_001161190.2 → NP_001154662.2 dicer-like 3 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001154662.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9LXW7

UniProtKB/TrEMBL

A0A5S9XHN9

Conserved Domains (5) summary

COG0571
Location:1200 → 1435

Rnc; dsRNA-specific ribonuclease [Transcription]

cd00046
Location:58 → 203

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.

cd00593
Location:1214 → 1361

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 ...

cd02844
Location:824 → 962

PAZ_CAF_like; PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA ...

pfam00271
Location:392 → 506

Helicase_C; Helicase conserved C-terminal domain
NM_114260.1 → NP_189978.1 dicer-like 3 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_189978.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9XHN9

Conserved Domains (5) summary

COG0571
Location:1151 → 1386

Rnc; dsRNA-specific ribonuclease [Transcription]

cd00046
Location:58 → 175

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.

cd00593
Location:1165 → 1312

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 ...

cd02844
Location:775 → 913

PAZ_CAF_like; PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA ...

pfam00271
Location:343 → 457

Helicase_C; Helicase conserved C-terminal domain
NM_001339116.1 → NP_001325813.1 dicer-like 3 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1I9LMD4, A0A5S9XHN9