DCL1 is the Arabidopsis nuclear Dicer-like RNase III enzyme that processes structured pri- and pre-miRNA hairpins into miRNA/miRNA-star duplexes. It works with DRB1/HYL1, SERRATE, and other nuclear microprocessor factors in D-bodies to control the precision and efficiency of plant miRNA biogenesis. Developmental, antiviral, lsiRNA, ta-siRNA, and seed/flower phenotypes arise mainly from this nuclear small-RNA processing role rather than from separate primary functions.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: In vitro dsDNA binding by the DCL1 dsRBDs was later demonstrated experimentally (PMID:26101256), but DNA binding remains peripheral to the miRNA-processing function. Reason: Although this row is an electronic InterPro mapping, direct experimental dsDNA binding by the DCL1 dsRBDs was measured in PMID:26101256, so removal on the grounds that no DNA-binding evidence exists would be incorrect. DNA binding has no established role in DCL1 biology, whose core function is nuclear pri-/pre-miRNA recognition and cleavage, so the term is kept as non-core. |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | MODIFY | Summary: DCL1 binds RNA hairpin substrates during miRNA precursor processing. Reason: RNA binding is true but less specific than DCL1 ribonuclease III activity and double-stranded RNA binding in pri-/pre-miRNA processing. Proposed replacements: ribonuclease III activity double-stranded RNA binding |
| GO:0004525 ribonuclease III activity | IEA GO_REF:0000002 | ACCEPT | Summary: DCL1 is the RNase III enzyme of the Arabidopsis nuclear miRNA microprocessor. Reason: RNase III activity is the core catalytic molecular function by which DCL1 cleaves pri-/pre-miRNA hairpins. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md Falcon synthesis identifies DCL1 as the nuclear RNase III enzyme that catalyzes miRNA precursor processing. file:ARATH/DCL1/DCL1-uniprot.txt Ribonuclease (RNase) III involved in RNA-mediated post-transcriptional gene silencing (PTGS). file:interpro/panther/PTHR14950/PTHR14950-entries.csv Q9SP32,Endoribonuclease Dicer homolog 1 |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: DCL1 carries helicase/ATP-binding domain features. Reason: ATP binding is plausible from domain architecture, but the curated core function is RNase III-mediated miRNA precursor cleavage. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: DCL1 functions in the nucleus during plant miRNA biogenesis. Reason: Nuclear D-body localization is directly tied to DCL1 microprocessor activity. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md Falcon synthesis describes DCL1/HYL1/SERRATE nuclear D-bodies as the miRNA-processing context. file:ARATH/DCL1/DCL1-uniprot.txt Localizes to nuclear dicing body (also named D body), a nuclear body distributed throughout the nucleoplasm and involved in miRNA processing. |
| GO:0006364 rRNA processing | IEA GO_REF:0000002 | REMOVE | Summary: rRNA processing appears to be inherited from broad RNase III/InterPro family context rather than Arabidopsis DCL1 biology. Reason: DCL1 literature and UniProt function support miRNA/siRNA precursor processing, not a primary rRNA-processing role. |
| GO:0006396 RNA processing | IEA GO_REF:0000002 | MODIFY | Summary: RNA processing is directionally related to DCL1 RNA nuclease activity but is less specific than RNase III/miRNA processing terms. Reason: Use DCL1-specific ribonuclease III activity and primary miRNA processing rather than broad RNA processing or generic hydrolase activity. Proposed replacements: ribonuclease III activity primary miRNA processing |
| GO:0009616 RNAi-mediated antiviral immune response | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: DCL1 can generate 21-nt siRNAs from CaMV leader-derived substrates, but DCL4 is the major VIGS/RNA-virus antiviral Dicer and UniProt notes DCL1 can repress antiviral silencing via DCL4/DCL3 regulation. Reason: The viral-siRNA evidence supports a specialized, non-core antiviral RNAi contribution rather than making DCL1 the central antiviral RNAi Dicer. DCL1 core function remains nuclear miRNA precursor processing. Supporting Evidence: PMID:17090584 Specifically, DCL1 generates 21 nt siRNAs from the CaMV leader region. file:ARATH/DCL1/DCL1-uniprot.txt Represses antiviral RNA silencing through negative regulation of the expression of DCL4 and DCL3. |
| GO:0010267 ta-siRNA processing | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: DCL1 contributes indirectly to trans-acting siRNA pathways by producing initiating miRNAs for TAS transcripts. Reason: This pathway role is supported, but DCL1 does not directly process ta-siRNA duplexes; its contribution is upstream through miRNA biogenesis, so the core function remains nuclear pri-/pre-miRNA cleavage. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | MODIFY | Summary: hydrolase activity is directionally related to DCL1 RNA nuclease activity but is less specific than RNase III/miRNA processing terms. Reason: Use DCL1-specific ribonuclease III activity and primary miRNA processing rather than broad RNA processing or generic hydrolase activity. Proposed replacements: ribonuclease III activity primary miRNA processing |
| GO:0016891 RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism | IEA GO_REF:0000002 | MODIFY | Summary: RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism is directionally related to DCL1 RNA nuclease activity but is less specific than RNase III/miRNA processing terms. Reason: Use DCL1-specific ribonuclease III activity and primary miRNA processing rather than broad RNA processing or generic hydrolase activity. Proposed replacements: ribonuclease III activity primary miRNA processing |
| GO:0035196 miRNA processing | IEA GO_REF:0000117 | MODIFY | Summary: DCL1 is part of miRNA biogenesis through precursor cleavage. Reason: The more precise process term for DCL1 is primary miRNA processing. Proposed replacements: primary miRNA processing |
| GO:0005515 protein binding | IPI PMID:15821876 Specific interactions between Dicer-like proteins and HYL1/D... | MARK AS OVER ANNOTATED | Summary: The cited interactions involve DCL1 partners such as DRB/HYL-family proteins and miRNA-biogenesis cofactors. Reason: Generic protein binding obscures the relevant biology: DCL1 operates in a nuclear miRNA-processing complex with specific partners. |
| GO:0005515 protein binding | IPI PMID:16428603 The interaction between DCL1 and HYL1 is important for effic... | MARK AS OVER ANNOTATED | Summary: The cited interactions involve DCL1 partners such as DRB/HYL-family proteins and miRNA-biogenesis cofactors. Reason: Generic protein binding obscures the relevant biology: DCL1 operates in a nuclear miRNA-processing complex with specific partners. |
| GO:0005515 protein binding | IPI PMID:18632581 The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in h... | MARK AS OVER ANNOTATED | Summary: The cited interactions involve DCL1 partners such as DRB/HYL-family proteins and miRNA-biogenesis cofactors. Reason: Generic protein binding obscures the relevant biology: DCL1 operates in a nuclear miRNA-processing complex with specific partners. |
| GO:0010267 ta-siRNA processing | IMP PMID:15469823 Endogenous trans-acting siRNAs regulate the accumulation of ... | KEEP AS NON CORE | Summary: DCL1 contributes indirectly to trans-acting siRNA pathways by producing initiating miRNAs for TAS transcripts. Reason: This pathway role is supported, but DCL1 does not directly process ta-siRNA duplexes; its contribution is upstream through miRNA biogenesis, so the core function remains nuclear pri-/pre-miRNA cleavage. |
| GO:0003677 DNA binding | EXP PMID:26101256 Induced folding in RNA recognition by Arabidopsis thaliana D... | KEEP AS NON CORE | Summary: PMID:26101256 directly measures dsDNA binding by the DCL1 dsRBDs by fluorescence anisotropy, so the annotation is experimentally supported, though DNA binding is peripheral to the miRNA-processing function. Reason: The cached full text of PMID:26101256 explicitly demonstrates DNA binding ("We found that both constructs do bind dsDNA", with measured affinities of roughly 600-860 nM for DCL1-A, DCL1-B and DCL1-AB), so the annotation is not a mis-citation and should not be removed. However, in vitro dsDNA binding by isolated dsRBDs has no established role in DCL1 biology, whose core function is nuclear pri-/pre-miRNA recognition and cleavage, so the term is kept as non-core. Supporting Evidence: PMID:26101256 We found that both constructs do bind dsDNA, showing that DCL1-A is also peculiar in terms of nucleic acid recognition with respect to other dsRBDs |
| GO:0003677 DNA binding | IDA PMID:26101256 Induced folding in RNA recognition by Arabidopsis thaliana D... | KEEP AS NON CORE | Summary: PMID:26101256 directly measures dsDNA binding by the DCL1 dsRBDs by fluorescence anisotropy, so the annotation is experimentally supported, though DNA binding is peripheral to the miRNA-processing function. Reason: The cached full text of PMID:26101256 explicitly demonstrates DNA binding ("We found that both constructs do bind dsDNA", with measured affinities of roughly 600-860 nM for DCL1-A, DCL1-B and DCL1-AB), so the annotation is not a mis-citation and should not be removed. However, in vitro dsDNA binding by isolated dsRBDs has no established role in DCL1 biology, whose core function is nuclear pri-/pre-miRNA recognition and cleavage, so the term is kept as non-core. Supporting Evidence: PMID:26101256 We found that both constructs do bind dsDNA, showing that DCL1-A is also peculiar in terms of nucleic acid recognition with respect to other dsRBDs |
| GO:0003725 double-stranded RNA binding | EXP PMID:26101256 Induced folding in RNA recognition by Arabidopsis thaliana D... | ACCEPT | Summary: DCL1 binds structured double-stranded regions in pri-/pre-miRNA substrates. Reason: Double-stranded RNA binding supports DCL1 substrate recognition in the miRNA-processing complex. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md DCL1 processes fold-back pri-/pre-miRNA hairpins into miRNA duplexes. |
| GO:0003725 double-stranded RNA binding | IPI PMID:26101256 Induced folding in RNA recognition by Arabidopsis thaliana D... | ACCEPT | Summary: DCL1 binds structured double-stranded regions in pri-/pre-miRNA substrates. Reason: Double-stranded RNA binding supports DCL1 substrate recognition in the miRNA-processing complex. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md DCL1 processes fold-back pri-/pre-miRNA hairpins into miRNA duplexes. |
| GO:0005737 cytoplasm | ISM GO_REF:0000122 | REMOVE | Summary: DCL1 core localization evidence is nuclear/nuclear dicing body rather than cytoplasmic. Reason: The GOA cytoplasm row is prediction/inference context, while accessible DCL1 publications and UniProt place DCL1 in the nucleus and D-bodies for miRNA processing. |
| GO:0005515 protein binding | IPI PMID:29982637 SMA1, a homolog of the splicing factor Prp28, has a multifac... | MARK AS OVER ANNOTATED | Summary: The cited interactions involve DCL1 partners such as DRB/HYL-family proteins and miRNA-biogenesis cofactors. Reason: Generic protein binding obscures the relevant biology: DCL1 operates in a nuclear miRNA-processing complex with specific partners. |
| GO:0048317 seed morphogenesis | IMP PMID:24784759 Global Regulation of Embryonic Patterning in Arabidopsis by ... | KEEP AS NON CORE | Summary: DCL1 mutants affect seed morphogenesis. Reason: The developmental process is a downstream consequence of miRNA-biogenesis defects, not a distinct molecular/core role of DCL1. |
| GO:0000911 cytokinesis by cell plate formation | IMP PMID:10556049 Disruption of an RNA helicase/RNAse III gene in Arabidopsis ... | MODIFY | Summary: The cited sus1/dcl1 floral meristem phenotype reflects abnormal meristem cell proliferation, not direct cytokinesis by cell plate formation. Reason: Cell plate formation is too mechanistic for the available evidence. The supported interpretation is a downstream flower/floral-meristem developmental phenotype caused by DCL1-dependent RNA processing defects. Proposed replacements: flower development |
| GO:2000034 regulation of seed maturation | IMP PMID:21330492 MicroRNAs regulate the timing of embryo maturation in Arabid... | KEEP AS NON CORE | Summary: DCL1 mutants affect regulation of seed maturation. Reason: The developmental process is a downstream consequence of miRNA-biogenesis defects, not a distinct molecular/core role of DCL1. |
| GO:0010599 lsiRNA processing | IMP PMID:18003861 A novel class of bacteria-induced small RNAs in Arabidopsis. | KEEP AS NON CORE | Summary: DCL1 contributes to lsiRNA processing through miRNA/nat-siRNA precursor-processing pathways. Reason: This pathway role is supported, but it is downstream or specialized relative to the core DCL1 activity of nuclear miRNA precursor cleavage. |
| GO:0009616 RNAi-mediated antiviral immune response | IMP PMID:17090584 Four plant Dicers mediate viral small RNA biogenesis and DNA... | KEEP AS NON CORE | Summary: DCL1 can generate 21-nt siRNAs from CaMV leader-derived substrates, but DCL4 is the major VIGS/RNA-virus antiviral Dicer and UniProt notes DCL1 can repress antiviral silencing via DCL4/DCL3 regulation. Reason: The viral-siRNA evidence supports a specialized, non-core antiviral RNAi contribution rather than making DCL1 the central antiviral RNAi Dicer. DCL1 core function remains nuclear miRNA precursor processing. Supporting Evidence: PMID:17090584 Specifically, DCL1 generates 21 nt siRNAs from the CaMV leader region. file:ARATH/DCL1/DCL1-uniprot.txt Represses antiviral RNA silencing through negative regulation of the expression of DCL4 and DCL3. |
| GO:0010445 nuclear dicing body | IDA PMID:17442570 Identification of nuclear dicing bodies containing proteins ... | ACCEPT | Summary: DCL1 functions in the nuclear dicing body during plant miRNA biogenesis. Reason: Nuclear D-body localization is directly tied to DCL1 microprocessor activity. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md Falcon synthesis describes DCL1/HYL1/SERRATE nuclear D-bodies as the miRNA-processing context. file:ARATH/DCL1/DCL1-uniprot.txt Localizes to nuclear dicing body (also named D body), a nuclear body distributed throughout the nucleoplasm and involved in miRNA processing. |
| GO:0010267 ta-siRNA processing | IMP PMID:16699516 Dissecting Arabidopsis thaliana DICER function in small RNA ... | KEEP AS NON CORE | Summary: DCL1 contributes indirectly to trans-acting siRNA pathways by producing initiating miRNAs for TAS transcripts. Reason: This pathway role is supported, but DCL1 does not directly process ta-siRNA duplexes; its contribution is upstream through miRNA biogenesis, so the core function remains nuclear pri-/pre-miRNA cleavage. |
| GO:0005634 nucleus | IDA PMID:17369351 Arabidopsis primary microRNA processing proteins HYL1 and DC... | ACCEPT | Summary: DCL1 functions in the nucleus during plant miRNA biogenesis. Reason: Nuclear D-body localization is directly tied to DCL1 microprocessor activity. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md Falcon synthesis describes DCL1/HYL1/SERRATE nuclear D-bodies as the miRNA-processing context. file:ARATH/DCL1/DCL1-uniprot.txt Localizes to nuclear dicing body (also named D body), a nuclear body distributed throughout the nucleoplasm and involved in miRNA processing. |
| GO:0003725 double-stranded RNA binding | IDA PMID:15821876 Specific interactions between Dicer-like proteins and HYL1/D... | ACCEPT | Summary: DCL1 binds structured double-stranded regions in pri-/pre-miRNA substrates. Reason: Double-stranded RNA binding supports DCL1 substrate recognition in the miRNA-processing complex. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md DCL1 processes fold-back pri-/pre-miRNA hairpins into miRNA duplexes. |
| GO:0005634 nucleus | IDA PMID:15821876 Specific interactions between Dicer-like proteins and HYL1/D... | ACCEPT | Summary: DCL1 functions in the nucleus during plant miRNA biogenesis. Reason: Nuclear D-body localization is directly tied to DCL1 microprocessor activity. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md Falcon synthesis describes DCL1/HYL1/SERRATE nuclear D-bodies as the miRNA-processing context. file:ARATH/DCL1/DCL1-uniprot.txt Localizes to nuclear dicing body (also named D body), a nuclear body distributed throughout the nucleoplasm and involved in miRNA processing. |
| GO:0006396 RNA processing | ISS PMID:12225663 CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, ... | MODIFY | Summary: RNA processing is directionally related to DCL1 RNA nuclease activity but is less specific than RNase III/miRNA processing terms. Reason: Use DCL1-specific ribonuclease III activity and primary miRNA processing rather than broad RNA processing or generic hydrolase activity. Proposed replacements: ribonuclease III activity primary miRNA processing |
| GO:0009880 embryonic pattern specification | IMP PMID:8787738 SHORT INTEGUMENT (SIN1), a gene required for ovule developme... | KEEP AS NON CORE | Summary: DCL1 mutants affect embryonic pattern specification. Reason: The developmental process is a downstream consequence of miRNA-biogenesis defects, not a distinct molecular/core role of DCL1. |
| GO:0010228 vegetative to reproductive phase transition of meristem | IMP PMID:8787738 SHORT INTEGUMENT (SIN1), a gene required for ovule developme... | KEEP AS NON CORE | Summary: DCL1 mutants affect vegetative to reproductive phase transition of meristem. Reason: The developmental process is a downstream consequence of miRNA-biogenesis defects, not a distinct molecular/core role of DCL1. |
| GO:0031053 primary miRNA processing | TAS PMID:16144699 MicroRNA biogenesis and function in plants. | ACCEPT | Summary: DCL1 cleaves primary miRNA precursors in the nuclear microprocessor. Reason: Primary miRNA processing is the best-supported core biological process for DCL1. Supporting Evidence: file:ARATH/DCL1/DCL1-deep-research-falcon.md DCL1 processes pri-miRNAs in the nucleus to release a miRNA/miRNA-star duplex. file:ARATH/DCL1/DCL1-uniprot.txt Functions in the microRNAs (miRNAs) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). |
| GO:0035279 miRNA-mediated gene silencing by mRNA destabilization | IMP PMID:15851028 microRNA-directed phasing during trans-acting siRNA biogenes... | MODIFY | Summary: DCL1 produces miRNAs that can mediate target mRNA destabilization, but DCL1 is not the AGO effector executing target repression. Reason: Primary miRNA processing captures the DCL1 step more accurately than the downstream target-silencing output. Proposed replacements: primary miRNA processing |
| GO:0009908 flower development | TAS PMID:8787738 SHORT INTEGUMENT (SIN1), a gene required for ovule developme... | KEEP AS NON CORE | Summary: DCL1 mutants affect flower development. Reason: The developmental process is a downstream consequence of miRNA-biogenesis defects, not a distinct molecular/core role of DCL1. |
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Download this section (compressed HTML)Q: Should broad DCL1 RNA-processing annotations be replaced consistently with primary miRNA processing where the evidence is microprocessor activity?
Q: Is the rRNA-processing InterPro transfer for plant Dicer-like proteins obsolete or overly broad for DCL1 curation?
Experiment: Reconstitute DCL1-HYL1-SERRATE processing on representative Arabidopsis pri-miRNAs to compare cleavage precision across precursor structures.
Experiment: Map active DCL1 complexes in nuclear D-bodies versus nucleoplasm using tagged endogenous DCL1 and substrate-specific processing assays.
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