DRB1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004525 ribonuclease III activity	IBA GO_REF:0000033	REMOVE	Summary: DRB1/HYL1 binds RNA and stimulates the catalytic RNase III DCL1; it does not itself carry out RNase III cleavage. Reason: The PAINT table places GO:0004525 at PTN000129453, but HYL1 has tandem dsRNA-binding domains rather than an RNase III catalytic domain. Recombinant processing assays assign cleavage to DCL1 and increased rate/accuracy to HYL1 (PMID:18632569). This target-specific domain architecture contradicts transfer of catalysis; donor count is not the issue. The completed OpenScientist hypothesis report independently agrees with this catalytic/cofactor distinction. Primary Results show that adding HYL1 alone to DCL1 increases cleavage rate and precise processing; they are not an explicit negative HYL1-alone nuclease assay. The report does not establish an exact SF0-to-SF1 propagation path or a de novo catalytic-domain scan; neither claim is needed for this decision. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN000129453 · PTN000129453 SUPPORTS SOURCE BUT NOT TARGET The cached PTHR11207 PAINT table directly records a GO:0004525 IBD at this node with experimentally grounded nuclease seeds. HYL1 lacks the catalytic RNase III domain. This challenges scope of the ancestral assertion for a dsRBD-only target; it does not claim that the listed seeds are wrong or infer an unverified history of domain loss. The local entries table confirms O04492 in SF1 and P0A7Y0/Q9NRR4 in SF0, but subfamily membership does not locate the ancestral assertion or its pruning boundaries. The PAINT table also contains RNase III IRD exclusions at other nodes; no family-wide unrestricted propagation is asserted here. Supporting Evidence: PMID:18632569 We show that recombinant HYL1 and SE proteins accelerate the rate of DCL1-mediated cleavage of pre- and pri-miR167b substrates and promote accurate processing. PMID:18632569 Addition of either recombinant HYL1 or recombinant SE significantly increased the initial rate of DCL1-mediated cleavage of pre-miR167b to 21-nt small RNAs
GO:0003725 double-stranded RNA binding	IEA GO_REF:0000002	ACCEPT	Summary: DRB1/HYL1 binds double-stranded regions of pri-/pre-miRNA substrates through its dsRNA-binding domains. Reason: Double-stranded RNA binding is the core molecular function of DRB1/HYL1. Supporting Evidence: PMID:15821876 DCL1, DCL3, HYL1 and the four HYL1 homologs exhibit significant dsRNA-binding activity
GO:0003725 double-stranded RNA binding	IEA GO_REF:0000117	ACCEPT	Summary: DRB1/HYL1 binds double-stranded regions of pri-/pre-miRNA substrates through its dsRNA-binding domains. Reason: Double-stranded RNA binding is the core molecular function of DRB1/HYL1. Supporting Evidence: PMID:15821876 DCL1, DCL3, HYL1 and the four HYL1 homologs exhibit significant dsRNA-binding activity
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: DRB1/HYL1 localizes to nucleus in the miRNA-processing context. Reason: Direct HYL1 localization experiments support nuclear function, including diffuse nucleoplasmic and dicing-body pools (PMID:11148283; PMID:17442570). Supporting Evidence: PMID:17442570 Using live-cell imaging, we show here that DCL1 and HYL1 colocalize in discrete nuclear bodies in addition to being present in a low-level diffuse nucleoplasmic distribution.
GO:0016607 nuclear speck	IEA GO_REF:0000044	ACCEPT	Summary: DRB1/HYL1 localizes to nuclear speck in the miRNA-processing context. Reason: HYL1 interactions in nuclear splicing speckles are explicitly observed in PMID:26227967. Do not treat nuclear speckles and nuclear dicing bodies as interchangeable solely because both appear punctate. Supporting Evidence: PMID:26227967 all of these splicing-related factors directly interact with both HYL1 and SE in nuclear splicing speckles.
GO:0005515 protein binding	IPI PMID:15821876 Specific interactions between Dicer-like proteins and HYL1/D...	REMOVE	Summary: The generic protein-interaction annotation adds no functional information beyond independently annotated HYL1 RNA-binding activity. Reason: Remove this uninformative protein-binding annotation without disputing the reported interaction. Double-stranded RNA binding is already represented by appropriate direct RNA-binding annotations in this review. Redirecting the IPI protein-interaction row to that different assay would conflate evidence types and add redundant functional coverage. Supporting Evidence: PMID:15821876 DCL1, DCL3, HYL1 and the four HYL1 homologs exhibit significant dsRNA-binding activity
GO:0005515 protein binding	IPI PMID:16428603 The interaction between DCL1 and HYL1 is important for effic...	MODIFY	Summary: DCL1-HYL1 association promotes efficient and accurate miRNA-precursor cleavage. Reason: Binding coupled to stimulation of DCL1 supports ribonuclease activator activity. The source genetic and interaction experiments are corroborated by direct recombinant-protein rate measurements in PMID:18632569; HYL1 is an activator, not the catalytic nuclease. Proposed replacements: ribonuclease activator activity Supporting Evidence: PMID:16428603 These results indicate that HYL1 has a function in assisting efficient and precise cleavage of pri-miRNA through interaction with DCL1. PMID:18632569 We show that recombinant HYL1 and SE proteins accelerate the rate of DCL1-mediated cleavage of pre- and pri-miR167b substrates and promote accurate processing.
GO:0005515 protein binding	IPI PMID:20462493 Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecula...	REMOVE	Summary: The generic protein-interaction annotation adds no functional information beyond independently annotated HYL1 RNA-binding activity. Reason: Remove this uninformative protein-binding annotation without disputing the reported interaction. Double-stranded RNA binding is already represented by appropriate direct RNA-binding annotations in this review. Redirecting the IPI protein-interaction row to that different assay would conflate evidence types and add redundant functional coverage. Supporting Evidence: PMID:20462493 both HR1 and TR2 are canonical dsRBDs for dsRNA binding, whereas HR2 of HYL1 is a non-canonical dsRBD harboring a putative dimerization interface.
GO:0005515 protein binding	IPI PMID:21798944 Evidence for network evolution in an Arabidopsis interactome...	REMOVE	Summary: Arabidopsis Interactome-1 is a high-throughput yeast two-hybrid map of 5,664 binary interactions. The HYL1 edge recorded by this IPI row is in the supplementary interaction table, not the main text. Reason: The specific HYL1 partner is listed only in the supplementary dataset, which is a feature of a systematic screen and not evidence against the curator's row. A single systematic Y2H edge does not establish a more informative molecular function than the dsRNA-binding and microprocessor activities already annotated. Consistent with the other HYL1 protein-binding rows in this review, the generic term is removed. This does not dispute the interaction. Supporting Evidence: PMID:21798944 Confirmed pairs were assembled into a dataset of 5,664 binary interactions between 2,661 proteins, called Arabidopsis Interactome version 1 “main screen” (AI-1MAIN) (table S4).
GO:0005515 protein binding	IPI PMID:23141542 Fast-forward genetics identifies plant CPL phosphatases as r...	REMOVE	Summary: CPL1 reaches HYL1 through a SERRATE scaffold and regulates HYL1 phosphorylation. Reason: Remove generic protein binding because it lacks functional information. The interaction is supported and is retained in the evidence narrative; removal does not mean it is false. These interaction/regulatory experiments do not establish a more specific molecular activity of HYL1 by themselves. Supporting Evidence: PMID:23141542 In the miRNA processing complex, SE functions as a scaffold to mediate CPL1 interaction with HYL1, which needs to be dephosphorylated for optimal activity.
GO:0005515 protein binding	IPI PMID:29769717 SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to imp...	REMOVE	Summary: Wang et al. (2018) show that the SWI/SNF ATPase CHR2/BRM partners the microprocessor component Serrate and remodels pri-miRNAs, preventing their processing by DCL1 and HYL1. The IPI row records a HYL1 interaction tested within this microprocessor study. Reason: The cached record is abstract-only, and the HYL1-specific interaction assay (most likely with SE or CHR2 in the microprocessor context) is not described in the abstract. That is not evidence against the curator. In either case the generic protein-binding term adds nothing beyond the microprocessor, dsRNA-binding and pre-miRNA processing annotations that capture HYL1's role. It is removed, consistent with the other protein-binding rows in this review, without disputing the interaction. Supporting Evidence: PMID:29769717 We conclude that CHR2 accesses pri-miRNAs through SE and remodels their secondary structures, preventing downstream processing by DCL1 and HYL1.
GO:0005515 protein binding	IPI PMID:32612234 Extensive signal integration by the phytohormone protein net...	REMOVE	Summary: Altmann et al. (2020) mapped more than 2,000 binary interactions in the Arabidopsis phytohormone signaling network. The HYL1 edge recorded by this row is in the supplementary dataset. Reason: This is a systematic binary interaction screen whose individual edges are listed in supplementary data. The abstract's lack of an enumerated HYL1 partner is not evidence against the curator. A single network edge does not support a more informative molecular function than HYL1's established dsRNA-binding microprocessor role, so the generic term is removed, consistent with the other protein-binding rows. This does not dispute the interaction. Supporting Evidence: PMID:32612234 Here, we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions.
GO:0042802 identical protein binding	IPI PMID:15821876 Specific interactions between Dicer-like proteins and HYL1/D...	KEEP AS NON CORE	Summary: HYL1 self-association is supported by biochemical and structural evidence. Reason: Retain self-association as mechanistic context for RNA-substrate recognition; the defining molecular roles are RNA binding and activation of DCL1 cleavage. Supporting Evidence: PMID:20462493 The dimerization of HYL1 was further confirmed by in vitro pull-down, coimmunoprecipitation, and analytical gel filtration assays.
GO:0042802 identical protein binding	IPI PMID:20462493 Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecula...	KEEP AS NON CORE	Summary: HYL1 self-association is supported by biochemical and structural evidence. Reason: Retain self-association as mechanistic context for RNA-substrate recognition; the defining molecular roles are RNA binding and activation of DCL1 cleavage. Supporting Evidence: PMID:20462493 The dimerization of HYL1 was further confirmed by in vitro pull-down, coimmunoprecipitation, and analytical gel filtration assays.
GO:0016607 nuclear speck	EXP PMID:26227967 The RNA-binding protein HOS5 and serine/arginine-rich protei...	ACCEPT	Summary: DRB1/HYL1 localizes to nuclear speck in the miRNA-processing context. Reason: HYL1 interactions in nuclear splicing speckles are explicitly observed in PMID:26227967. Do not treat nuclear speckles and nuclear dicing bodies as interchangeable solely because both appear punctate. Supporting Evidence: PMID:26227967 all of these splicing-related factors directly interact with both HYL1 and SE in nuclear splicing speckles.
GO:0042659 regulation of cell fate specification	IGI PMID:37606225 Epigenetic regulation of female germline development through...	KEEP AS NON CORE	Summary: HYL1 and ERECTA genetically cooperate to restrict megaspore mother-cell identity in the ovule. Reason: The publisher full text of PMID:37606225 (Results, Fig. 8) directly tests er-119 hyl1 double mutants and detects multiple MMC-like cells, unlike either single mutant. Retain this well-supported developmental output as non-core; the evidence is not merely HYL1 transcription downstream of BZR1. Full-text access and a short exact excerpt are documented in DRB1-notes.md. Supporting Evidence: file:ARATH/DRB1/DRB1-notes.md ER and HYL1 genetically interact at the second checkpoint in MMC development and restrict a single MMC formation in each ovule.
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: DRB1/HYL1 localizes to nucleus in the miRNA-processing context. Reason: Direct HYL1 localization experiments support nuclear function, including diffuse nucleoplasmic and dicing-body pools (PMID:11148283; PMID:17442570). Supporting Evidence: PMID:17442570 Using live-cell imaging, we show here that DCL1 and HYL1 colocalize in discrete nuclear bodies in addition to being present in a low-level diffuse nucleoplasmic distribution.
GO:0005515 protein binding	IPI PMID:28586645 The Protein Phosphatase 4 and SMEK1 Complex Dephosphorylates...	REMOVE	Summary: PP4-SMEK1 targets HYL1 for dephosphorylation and controls its stability. Reason: Remove generic protein binding because it lacks functional information. The interaction is supported and is retained in the evidence narrative; removal does not mean it is false. These interaction/regulatory experiments do not establish a more specific molecular activity of HYL1 by themselves. Supporting Evidence: PMID:28586645 SMEK1 assembles a functional PP4 to target HYL1 for dephosphorylation.
GO:0005515 protein binding	IPI PMID:26227967 The RNA-binding protein HOS5 and serine/arginine-rich protei...	REMOVE	Summary: HOS5, RS40 and RS41 associate with HYL1 and SERRATE in nuclear speckles. Reason: Remove generic protein binding because it lacks functional information. The interaction is supported and is retained in the evidence narrative; removal does not mean it is false. These interaction/regulatory experiments do not establish a more specific molecular activity of HYL1 by themselves. Supporting Evidence: PMID:26227967 all of these splicing-related factors directly interact with both HYL1 and SE in nuclear splicing speckles.
GO:0010305 leaf vascular tissue pattern formation	IMP PMID:22623415 The microRNA pathway genes AGO1, HEN1 and HYL1 participate i...	KEEP AS NON CORE	Summary: DRB1/HYL1 mutants affect leaf vascular tissue pattern formation. Reason: This phenotype/process is a downstream output of altered miRNA biogenesis rather than a direct DRB1 function. Supporting Evidence: PMID:22623415 The abnormal vasculature of ago1 and hyl1 leaves also suggests a role for AGO1 and HYL1 in venation patterning.
GO:0010589 leaf proximal/distal pattern formation	IMP PMID:22623415 The microRNA pathway genes AGO1, HEN1 and HYL1 participate i...	KEEP AS NON CORE	Summary: DRB1/HYL1 mutants affect leaf proximal/distal pattern formation. Reason: This phenotype/process is a downstream output of altered miRNA biogenesis rather than a direct DRB1 function. Supporting Evidence: PMID:22623415 The morphological and histological characterization of these mutants and of dicer-like1-9 indicates that small RNAs participate in the proximal-distal and adaxial-abaxial patterning of leaves
GO:0031054 pre-miRNA processing	IMP PMID:16428603 The interaction between DCL1 and HYL1 is important for effic...	ACCEPT	Summary: DRB1/HYL1 promotes accurate pre-miRNA processing by assisting DCL1 on structured miRNA precursors. Reason: This process captures DRB1/HYL1 core biological role as a DCL1 microprocessor cofactor. Supporting Evidence: PMID:16428603 These results indicate that HYL1 has a function in assisting efficient and precise cleavage of pri-miRNA through interaction with DCL1.
GO:0031054 pre-miRNA processing	IMP PMID:17337628 The N-terminal double-stranded RNA binding domains of Arabid...	ACCEPT	Summary: DRB1/HYL1 promotes accurate pre-miRNA processing by assisting DCL1 on structured miRNA precursors. Reason: This process captures DRB1/HYL1 core biological role as a DCL1 microprocessor cofactor. Supporting Evidence: PMID:17337628 the N-terminal dsRBDs of HYL1 were sufficient for processing miRNA precursors and the generation of mature miRNA.
GO:0005515 protein binding	IPI PMID:16889646 SERRATE is a novel nuclear regulator in primary microRNA pro...	REMOVE	Summary: SERRATE physically associates with HYL1 during pri-miRNA processing. Reason: Remove generic protein binding because it lacks functional information. The interaction is supported and is retained in the evidence narrative; removal does not mean it is false. These interaction/regulatory experiments do not establish a more specific molecular activity of HYL1 by themselves. Supporting Evidence: PMID:16889646 We further demonstrate that SE is localized in the nucleus and interacts physically with HYL1.
GO:0010445 nuclear dicing body	IDA PMID:17442570 Identification of nuclear dicing bodies containing proteins ...	ACCEPT	Summary: DRB1/HYL1 localizes to nuclear dicing body in the miRNA-processing context. Reason: Nuclear and nuclear dicing body/speckle localization is tied to HYL1 function in pri-/pre-miRNA processing. Supporting Evidence: PMID:17442570 Using live-cell imaging, we show here that DCL1 and HYL1 colocalize in discrete nuclear bodies in addition to being present in a low-level diffuse nucleoplasmic distribution.
GO:0035198 miRNA binding	IDA PMID:17369351 Arabidopsis primary microRNA processing proteins HYL1 and DC...	MODIFY	Summary: The source detects association of HYL1 with primary miRNA precursors, not binding to a mature 21–23-nucleotide miRNA. Reason: QuickGO defines miRNA binding as binding the processed 21–23-nucleotide RNA. The co-immunoprecipitated substrates in PMID:17369351 are primary transcripts, so primary miRNA binding is a more faithful replacement than generic dsRNA binding. No inference about AGO-like activity is necessary. Proposed replacements: primary miRNA binding Supporting Evidence: PMID:17369351 The HYL1 protein coimmunoprecipitates with miR171a and miR159a precursors
GO:0005634 nucleus	IDA PMID:17369351 Arabidopsis primary microRNA processing proteins HYL1 and DC...	ACCEPT	Summary: DRB1/HYL1 localizes to nucleus in the miRNA-processing context. Reason: Direct HYL1 localization experiments support nuclear function, including diffuse nucleoplasmic and dicing-body pools (PMID:11148283; PMID:17442570). Supporting Evidence: PMID:17442570 Using live-cell imaging, we show here that DCL1 and HYL1 colocalize in discrete nuclear bodies in addition to being present in a low-level diffuse nucleoplasmic distribution.
GO:0015030 Cajal body	IDA NOT PMID:17369351 Arabidopsis primary microRNA processing proteins HYL1 and DC...	ACCEPT	Summary: The NOT Cajal-body annotation separates HYL1/DCL1 dicing bodies from Cajal bodies. Reason: The negated annotation is consistent with primary evidence that the DCL1/HYL1 nuclear body is distinct from Cajal bodies. Supporting Evidence: PMID:17369351 HYL1-mCherry and YFP-DCL1 fusion proteins colocalize to small nuclear bodies similar to Cajal bodies but lacking the Cajal body marker Atcoilin.
GO:0010267 ta-siRNA processing	IMP PMID:16889646 SERRATE is a novel nuclear regulator in primary microRNA pro...	KEEP AS NON CORE	Summary: DRB1/HYL1 influences ta-siRNA processing indirectly via miRNA biogenesis and initiating miRNA production. Reason: Retain the curator-supported pathway contribution as non-core, consistent with production of initiating miRNAs. The source abstract establishes SE/HYL1 pathway context, and the reviewed UniProt record specifically distinguishes indirect ta-siRNA production from direct precursor cleavage by HYL1. Supporting Evidence: file:ARATH/DRB1/DRB1-uniprot.txt Indirectly involved in the CC production of trans-acting small interfering RNAs (ta-siRNAs) derived CC from the TAS1, TAS2 or TAS3 endogenous transcripts by participating in CC the production of their initiating miRNAs.
GO:0003725 double-stranded RNA binding	IDA PMID:11148283 A mutation in the Arabidopsis HYL1 gene encoding a dsRNA bin...	ACCEPT	Summary: DRB1/HYL1 binds double-stranded regions of pri-/pre-miRNA substrates through its dsRNA-binding domains. Reason: Double-stranded RNA binding is the core molecular function of DRB1/HYL1. Supporting Evidence: PMID:11148283 We present evidence that the HYL1 gene is ABA-regulated and encodes a nuclear dsRNA binding protein.
GO:0003725 double-stranded RNA binding	IDA PMID:15821876 Specific interactions between Dicer-like proteins and HYL1/D...	ACCEPT	Summary: DRB1/HYL1 binds double-stranded regions of pri-/pre-miRNA substrates through its dsRNA-binding domains. Reason: Double-stranded RNA binding is the core molecular function of DRB1/HYL1. Supporting Evidence: PMID:15821876 DCL1, DCL3, HYL1 and the four HYL1 homologs exhibit significant dsRNA-binding activity
GO:0005634 nucleus	IDA PMID:11148283 A mutation in the Arabidopsis HYL1 gene encoding a dsRNA bin...	ACCEPT	Summary: DRB1/HYL1 localizes to nucleus in the miRNA-processing context. Reason: Direct HYL1 localization experiments support nuclear function, including diffuse nucleoplasmic and dicing-body pools (PMID:11148283; PMID:17442570). Supporting Evidence: PMID:11148283 We present evidence that the HYL1 gene is ABA-regulated and encodes a nuclear dsRNA binding protein.
GO:0009733 response to auxin	IMP PMID:11148283 A mutation in the Arabidopsis HYL1 gene encoding a dsRNA bin...	KEEP AS NON CORE	Summary: DRB1/HYL1 mutants affect response to auxin. Reason: This phenotype/process is a downstream output of altered miRNA biogenesis rather than a direct DRB1 function. Supporting Evidence: PMID:11148283 It also exhibits less sensitivity to auxin and cytokinin and hypersensitivity to abscisic acid (ABA).
GO:0009735 response to cytokinin	IMP PMID:11148283 A mutation in the Arabidopsis HYL1 gene encoding a dsRNA bin...	KEEP AS NON CORE	Summary: DRB1/HYL1 mutants affect response to cytokinin. Reason: This phenotype/process is a downstream output of altered miRNA biogenesis rather than a direct DRB1 function. Supporting Evidence: PMID:11148283 It also exhibits less sensitivity to auxin and cytokinin and hypersensitivity to abscisic acid (ABA).
GO:0009737 response to abscisic acid	IMP PMID:11148283 A mutation in the Arabidopsis HYL1 gene encoding a dsRNA bin...	KEEP AS NON CORE	Summary: DRB1/HYL1 mutants affect response to abscisic acid. Reason: This phenotype/process is a downstream output of altered miRNA biogenesis rather than a direct DRB1 function. Supporting Evidence: PMID:11148283 It also exhibits less sensitivity to auxin and cytokinin and hypersensitivity to abscisic acid (ABA).
GO:0035196 miRNA processing	IMP PMID:14972688 The nuclear dsRNA binding protein HYL1 is required for micro...	ACCEPT	Summary: DRB1/HYL1 promotes accurate miRNA processing by assisting DCL1 on structured miRNA precursors. Reason: This process captures DRB1/HYL1 core biological role as a DCL1 microprocessor cofactor. Supporting Evidence: PMID:14972688 miRNA accumulation also depends on the activity of HYL1, a nuclear dsRNA binding protein.
GO:0035279 miRNA-mediated gene silencing by mRNA destabilization	IMP PMID:15851028 microRNA-directed phasing during trans-acting siRNA biogenes...	KEEP AS NON CORE	Summary: DRB1/HYL1 influences miRNA-mediated gene silencing by mRNA destabilization indirectly via miRNA biogenesis and initiating miRNA production. Reason: Retain miRNA-directed target destabilization as a downstream silencing output supported directly by PMID:14972688. PMID:15851028 concerns miRNA-guided target cleavage and ta-siRNA phasing, but its accessible abstract does not expose the HYL1-specific experiment. HYL1 supports miRNA production rather than target-RNA cleavage catalysis. Supporting Evidence: PMID:14972688 reduced miRNA accumulation in hyl1 correlates with an increased accumulation of uncleaved target mRNAs
GO:0006357 regulation of transcription by RNA polymerase II	IMP PMID:37040378 Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Prop...	NEW	Summary: HYL1 supports proper MIR gene transcription and Pol II distribution independently of its established precursor-processing role. Reason: MIR-promoter reporter assays, genetic separation from processing defects, Pol II occupancy and HYL1 association support transcriptional regulation. These data do not by themselves establish sequence-specific DNA-binding transcription-factor activity. Supporting Evidence: PMID:37040378 Hence, our data support the idea that HYL1 is a direct positive regulator of MIR gene transcription.

Gene Description

Existing Annotations Review

Core Functions

Recognition of structured primary and precursor miRNAs by tandem dsRNA-binding domains supports accurate miRNA maturation; substrate requirements differ among MIR loci.

HYL1 binds the RNase III enzyme DCL1 and increases the rate and accuracy of miRNA-precursor cleavage as a noncatalytic activator.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

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OpenScientist

📚 Additional Documentation

Notes

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