DCL1 dicer-like 1 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: DCL1
Official Full Name: dicer-like 1
Primary source: TAIR:AT1G01040
Locus tag: AT1G01040
See related: Araport:AT1G01040
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: ABNORMAL SUSPENSOR 1; ASU1; ATDCL1; CAF; CARPEL FACTORY; dicer-like 1; DICER-LIKE 1; EMB60; EMB76; EMBRYO DEFECTIVE 60; EMBRYO DEFECTIVE 76; SHORT INTEGUMENTS 1; SIN1; SUS1; SUSPENSOR 1; T25K16.4; T25K16_4
Summary: Encodes a Dicer homolog. Dicer is a RNA helicase involved in microRNA processing. Mutations in this locus can result in embryo lethality. Embryo shape at seed maturity is globular-elongate. Other mutants convert the floral meristems to an indeterminate state, others yet show defects in ovule development. mRNA is expressed in all shoot tissues. DCL1 is able to produce miRNAs and siRNAs.
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Genomic context

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See DCL1 in Genome Data Viewer

Location:: chromosome: 1

Exon count:: 20

Sequence:: Chromosome: 1; NC_003070.9 (23121..31227)

Chromosome 1 - NC_003070.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structural determinants in the miRNA/miRNA* duplex and the DCL1 PAZ domain for precise and efficient plant miRNA processing.
Title: Structural determinants in the miRNA/miRNA* duplex and the DCL1 PAZ domain for precise and efficient plant miRNA processing.
Structural basis of microRNA processing by Dicer-like 1.
Title: Structural basis of microRNA processing by Dicer-like 1.
Light-stabilized FHA2 suppresses miRNA biogenesis through interactions with DCL1 and HYL1.
Title: Light-stabilized FHA2 suppresses miRNA biogenesis through interactions with DCL1 and HYL1.
The selection of these GC signatures was dependent on an RNA binding protein partner of DCL1 named HYL1.
Title: A conserved sequence signature is essential for robust plant miRNA biogenesis.
DDL is required for the optimal activity of DCL1.
Title: DAWDLE Interacts with DICER-LIKE Proteins to Mediate Small RNA Biogenesis.
DCL1 interacts with PIF4 which integrates miRNA biogenesis and red light signaling by regulating the transcription of a group of miRNA genes and the stability of DCL1 during dark-to-red-light or red-light-to-dark transitions.
Title: Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4.
Further analysis revealed that the steady state level of HYL1 protein in plants under osmotic stress is dependent on the SnRK2 kinases. Additionally, our results suggest that the SnRK2 kinases physically associate with the miRNA processing components SE and HYL1 and can phosphorylate these proteins in vitro.
Title: The SnRK2 kinases modulate miRNA accumulation in Arabidopsis.
Lariat RNAs localized in nuclear bodies, and partially co-localize with HYL1, and both DCL1 and HYL1 were mis-localized in dbr1-2... we thus propose that lariat RNAs, as decoys, inhibit miRNA processing, suggesting a hitherto unknown layer of regulation in miRNA biogenesis.
Title: Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis.
a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1.
Title: dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.
CDF2 binds preferentially to the pri-miRNAs regulated by itself and affects DCL1-mediated processing of these pri-miRNAs.
Title: The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs.

Submit: New GeneRIF Correction See all GeneRIFs (33)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

At1g01040_Arabidopsis_lyrata_ssp._lyrata_CAN1 (e-PCR)
- UniSTS:510254

At1g01040_Arabidopsis_lyrata_ssp._petraea_GER1 (e-PCR)
- UniSTS:510254

NM_001197952.1

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA 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
acts_upstream_of_or_within RNA processing	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within RNAi-mediated antiviral immune response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cytokinesis by cell plate formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within flower development	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within lsiRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within miRNA processing	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within miRNA-mediated gene silencing by mRNA destabilization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within primary miRNA processing	TAS Traceable Author Statement more info	PubMed
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of seed maturation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within seed morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within suspensor development	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within ta-siRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vegetative to reproductive phase transition of meristem	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	ISM Inferred from Sequence Model more info
located_in nuclear dicing body	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: dicer-like 1

NP_001184881.1

dicer-like 1 (DCL1); 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 3 (TAIR:AT3G43920.1).

NP_171612.1

dicer-like 1 (DCL1); 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), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), Dicer double-stranded RNA-binding fold (InterPro:IPR005034); BEST Arabidopsis thaliana protein match is: dicer-like 3 (TAIR:AT3G43920.2); Has 21958 Blast hits to 17420 proteins in 2982 species: Archae - 328; Bacteria - 11461; Metazoa - 3615; Fungi - 1668; Plants - 1373; Viruses - 45; Other Eukaryotes - 3468 (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_003070.9 Reference assembly

Range

23121..31227

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_099986.4 → NP_171612.1 dicer-like 1 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_171612.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9FDY6, Q9MAN0, Q9SP32

UniProtKB/TrEMBL

A0A178WCE6, A0A5S9RZI7, A0A654EAS8

Conserved Domains (8) summary

smart00358
Location:1734 → 1784

DSRM; Double-stranded RNA binding motif

cd00593
Location:1575 → 1730

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 post-transcriptional ...

cd02844
Location:1176 → 1320

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 ...

TIGR01622
Location:111 → 219

SF-CC1; splicing factor, CC1-like family

cd18802
Location:645 → 775

SF2_C_dicer; C-terminal helicase domain of the endoribonuclease Dicer

cd18034
Location:248 → 447

DEXHc_dicer; DEXH-box helicase domain of endoribonuclease Dicer

cd19869
Location:1837 → 1906

DSRM_DCL_plant; double-stranded RNA binding motif of plant Dicer-like proteins

pfam03368
Location:840 → 927

Dicer_dimer; Dicer dimerization domain
NM_001197952.1 → NP_001184881.1 dicer-like 1 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001184881.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9RZI7, F4HQG6

Conserved Domains (9) summary

smart00358
Location:1735 → 1785

DSRM; Double-stranded RNA binding motif

smart00487
Location:250 → 456

DEXDc; DEAD-like helicases superfamily

COG0571
Location:1558 → 1785

Rnc; dsRNA-specific ribonuclease [Transcription]

cd00046
Location:263 → 415

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:1576 → 1731

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:1177 → 1321

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:648 → 764

Helicase_C; Helicase conserved C-terminal domain

pfam03368
Location:841 → 927

Dicer_dimer; Dicer dimerization domain

cl00054
Location:1832 → 1905

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, ...