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

    Gene ID: 839574, updated on 2-Oct-2024

    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_003070.9Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene AP2/B3-like transcriptional factor family protein Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene pyrophosphorylase 1 Neighboring gene Homeodomain-like superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Structural basis of microRNA processing by Dicer-like 1. Wei X, et al. Nat Plants, 2021 Oct. PMID 34593993
    2. SHORT INTEGUMENT (SIN1), a gene required for ovule development in Arabidopsis, also controls flowering time. Ray A, et al. Development, 1996 Sep. PMID 8787738
    3. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Jacobsen SE, et al. Development, 1999 Dec. PMID 10556049
    4. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Park W, et al. Curr Biol, 2002 Sep 3. PMID 12225663, Free PMC Article
    5. MicroRNA biogenesis and function in plants. Chen X. FEBS Lett, 2005 Oct 31. PMID 16144699, Free PMC Article

    See all (54) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. Structural basis of microRNA processing by Dicer-like 1.
      Title: Structural basis of microRNA processing by Dicer-like 1.
    3. 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.
    4. 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.
    5. DDL is required for the optimal activity of DCL1.
      Title: DAWDLE Interacts with DICER-LIKE Proteins to Mediate Small RNA Biogenesis.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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)
    • At1g01040_Arabidopsis_lyrata_ssp._petraea_GER1 (e-PCR)
    NM_001197952.1

    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

    1. NC_003070.9 Reference assembly

      Range
      23121..31227
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    2. 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, ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SP32.2

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