HRDE-1 (heritable RNAi deficient 1, also WAGO-9) is a germline-specific nuclear Argonaute of the nematode-specific WAGO clade. It carries PAZ and PIWI domains but, like other WAGOs, lacks the slicer catalytic residues. HRDE-1 is loaded with RdRP-derived secondary 22G endo-siRNAs, including those produced downstream of piRNA (PRG-1/21U-RNA) and exogenous dsRNA targeting, and acts in germ-cell nuclei as the specificity factor of the nuclear RNAi (NRDE) pathway. siRNA-guided HRDE-1 recruits NRDE-2 to nascent target transcripts and, with NRDE-1/2/4 and the SET-25/SET-32/HPL-2 chromatin machinery, directs H3K9 trimethylation and co-transcriptional silencing of target loci. Acting in each inheriting generation, HRDE-1 propagates RNAi- and piRNA-initiated silencing across generations; it also visits perinuclear nuage, where it stimulates further small RNA amplification. Loss of HRDE-1 causes progressive loss of germline silencing and a temperature- sensitive mortal germline phenotype.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based (PAZ/PIWI/RNaseH-like) nucleic acid binding. HRDE-1 binds 22G siRNAs and, through them, nascent target RNAs. Reason: Very general but correct; HRDE-1 is an siRNA-binding Argonaute. More informative terms (siRNA binding) are captured elsewhere in this review. Supporting Evidence: PMID:22810588 HRDE-1 bound 22G endogenous (endo) siRNAs, which were expressed in germ cells |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: PAZ-domain-based RNA binding. Correct; HRDE-1 binds small RNA guides. Reason: Correct general MF; HRDE-1 co-precipitates exogenous-RNAi-induced and endogenous 22G siRNAs. Supporting Evidence: PMID:22810588 HRDE-1 co-precipitated with siRNAs for multiple generations after RNAi |
| GO:0003727 single-stranded RNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Argonaute-family IBA for single-stranded RNA binding. Argonautes bind their single-stranded small RNA guide and base-pair with single-stranded target RNA. Reason: Consistent with the conserved Argonaute PAZ/MID/PIWI guide-binding architecture retained in HRDE-1 and with its demonstrated binding of 22G siRNAs. Supporting Evidence: PMID:22810588 HRDE-1 bound 22G endogenous (endo) siRNAs, which were expressed in germ cells |
| GO:0004521 RNA endonuclease activity | IBA GO_REF:0000033 | REMOVE | Summary: Argonaute-family IBA for RNA endonuclease (slicer) activity. HRDE-1 belongs to the WAGO clade, whose members lack the catalytic residues required for slicing. Reason: Slicer activity was gained at an ancestral Argonaute node, but HRDE-1 is in the WAGO clade, which has lost it. Our alignment of HRDE-1 with human AGO2 found that none of the four DEDH catalytic tetrad positions (AGO2 D597, E637, D669, H807) is conserved. Shirayama et al. state that all WAGOs lack key catalytic residues. No cleavage activity has been reported for HRDE-1; it silences targets by nuclear recruitment of NRDE factors and chromatin modification. This is a target-specific loss of the inherited function, so the IBA should not apply. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN008584027 · PTN008584027 SUPPORTS SOURCE BUT NOT TARGET Argonaute node whose slicer assertion is right for catalytic AGO/PIWI members; the WAGO-clade HRDE-1 lacks the DEDH tetrad. Supporting Evidence: PMID:22738726 whereas the all WAGOs lack key catalytic residues file:worm/hrde-1/hrde-1-bioinformatics/RESULTS.md none of the four AGO2 slicer (DEDH) catalytic positions is |
| GO:0005634 nucleus | EXP PMID:22810588 A nuclear Argonaute promotes multigenerational epigenetic in... | ACCEPT | Summary: GFP::HRDE-1, which rescues the mutant, is expressed in nuclei of male and female germ cells. Reason: Core location; HRDE-1 acts on nascent transcripts and chromatin in germ-cell nuclei. Supporting Evidence: PMID:22810588 GFP::HRDE-1 was expressed in nuclei of male and female germ cells |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: IBA nuclear localization, consistent with experimental data. Reason: Directly confirmed experimentally for HRDE-1 by several groups. Supporting Evidence: PMID:22738726 we identified WAGO-9 (HRDE-1/C16C10.3) as a nuclear WAGO that is restricted to the germ line |
| GO:0005634 nucleus | IDA PMID:22738725 piRNAs can trigger a multigenerational epigenetic memory in ... | ACCEPT | Summary: Immunostaining with anti-HRDE-1/WAGO-9 antisera shows nuclear germline localization. Reason: Independent experimental confirmation of nuclear localization. Supporting Evidence: PMID:22738725 Using immunostaining, we show that it is expressed in the germline (Figure 2B), where it localizes to the nucleus (Figures 2C and 2D). |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to nucleus. Reason: Consistent with experimental evidence. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Argonaute-family IBA for cytoplasm. HRDE-1 is predominantly nuclear but also visits perinuclear nuage. Reason: HRDE-1 is predominantly nuclear, but it shuttles to perinuclear cytoplasmic nuage domains, where it stimulates small RNA amplification. Cytoplasmic presence is real but secondary to its nuclear role. Supporting Evidence: PMID:37083324 HRDE-1, while predominantly nuclear, also localizes to peri-nuclear nuage domains, where amplification is thought to occur. |
| GO:0007281 germ cell development | IMP PMID:22810588 A nuclear Argonaute promotes multigenerational epigenetic in... | KEEP AS NON CORE | Summary: hrde-1 mutants show a progressive, temperature-sensitive mortal germline phenotype, with late-generation animals failing to make mature gametes. Reason: The gametogenesis defect appears only after several generations without HRDE-1. It is a downstream result of the gradual loss of nuclear RNAi silencing in the germline, not a direct role in germ cell development. It is a real and important phenotype, so the annotation is kept as non-core. Supporting Evidence: PMID:22810588 Most late generation hrde-1(−) mutants (grown at 25°C) failed to produce mature oocytes or sperm PMID:22810588 In hrde-1- or nuclear RNAi-deficient animals, germline silencing is lost over generational time. |
| GO:0016442 RISC complex | IBA GO_REF:0000033 | MODIFY | Summary: Argonaute-family IBA for RISC complex. HRDE-1 forms siRNA-guided effector complexes on nascent nuclear transcripts rather than a classical cytoplasmic mRNA-cleaving RISC. Reason: HRDE-1 is a nuclear, non-slicing Argonaute. It acts on pre-mRNA and recruits NRDE-2, not on mature mRNAs in a cytoplasmic RISC. The broader parent RNAi effector complex (GO:0031332), already supported by IDA, describes its complexes better. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN001113179 · PTN001113179 SUPPORTS SOURCE BUT NOT TARGET RISC membership fits cytoplasmic AGO/ALG members; HRDE-1 forms nuclear siRNA effector complexes on nascent transcripts. Proposed replacements: RNAi effector complex Supporting Evidence: PMID:22810588 HRDE-1 was required for RNAi-mediated recruitment of NRDE-2 to a germline pre-mRNA |
| GO:0031332 RNAi effector complex | IDA PMID:22810588 A nuclear Argonaute promotes multigenerational epigenetic in... | ACCEPT | Summary: HRDE-1 associates with siRNAs in germ cells and forms the siRNA-guided effector of germline nuclear RNAi. Reason: HRDE-1/siRNA complexes are the effector complexes of germline nuclear RNAi. Supporting Evidence: PMID:22810588 hrde-1 encodes an Argonaute protein that associates with small interfering RNAs in the germ cells of progeny of animals exposed to double-stranded RNA |
| GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing | IBA GO_REF:0000033 | MODIFY | Summary: Argonaute-family IBA for post-transcriptional silencing. HRDE-1 silences its targets co-transcriptionally in the nucleus. Reason: Many Argonautes carry out post-transcriptional silencing, so the inference is reasonable at the family level. For HRDE-1, however, the experimental data show nuclear, co-transcriptional silencing with H3K9me3 deposition. Its process is better captured by regulatory ncRNA-mediated heterochromatin formation, matching the change made to the IMP annotation. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN001113179 · PTN001113179 SUPPORTS SOURCE BUT NOT TARGET PTGS is correct for many family members; HRDE-1 silences co-transcriptionally through the NRDE pathway and H3K9me3. Proposed replacements: regulatory ncRNA-mediated heterochromatin formation Supporting Evidence: PMID:22810588 indicating that the RNAi inheritance machinery silences germline target genes co-transcriptionally during the normal course of reproduction |
| GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing | IMP PMID:22810588 A nuclear Argonaute promotes multigenerational epigenetic in... | MODIFY | Summary: hrde-1 mutants silence targets on direct dsRNA exposure but fail to pass the silencing to progeny. The silencing HRDE-1 directs is nuclear and co-transcriptional. Reason: The mutant phenotype is real, but the mechanism is not post-transcriptional. HRDE-1 directs H3K9me3 and co-transcriptional silencing at target loci, which the module also captures as regulatory ncRNA-mediated heterochromatin formation. The NRDE-2 annotation sets the precedent of GO:0031048 for this pathway. Proposed replacements: regulatory ncRNA-mediated heterochromatin formation Supporting Evidence: PMID:22810588 In the nuclei of these germ cells, HRDE-1 engages the nuclear RNAi defective pathway to direct the trimethylation of histone H3 at Lys 9 (H3K9me3) at RNAi-targeted genomic loci and promote RNAi inheritance. PMID:37083324 Tethering the nuclear Argonaute WAGO-9/HRDE-1 induces heterochromatin formation and independently induces small RNA amplification. |
| GO:0035198 miRNA binding | IBA GO_REF:0000033 | MODIFY | Summary: Argonaute-family IBA for miRNA binding. HRDE-1 is loaded with RdRP-derived 22G siRNAs, not miRNAs. Reason: miRNA binding comes from the ALG/AGO clade. HRDE-1 is a WAGO, and its sequenced small RNA partners are 22G endo-siRNAs and exogenous-RNAi-derived siRNAs. siRNA binding (GO:0035197) is the correct small-RNA-binding term. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN001113179 · PTN001113179 SUPPORTS SOURCE BUT NOT TARGET miRNA binding reflects ALG/AGO-clade members; WAGO HRDE-1 binds RdRP-derived 22G siRNAs. Proposed replacements: siRNA binding Supporting Evidence: PMID:22810588 HRDE-1 bound 22G endogenous (endo) siRNAs, which were expressed in germ cells |
| GO:0036464 cytoplasmic ribonucleoprotein granule | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Argonaute-family IBA for cytoplasmic RNP granule. HRDE-1 localizes partly to perinuclear nuage (Mutator foci). Reason: Supported by the observed nuage/Mutator-focus localization of HRDE-1. This is secondary to its predominantly nuclear localization. Supporting Evidence: PMID:37083324 HRDE-1, while predominantly nuclear, also localizes to peri-nuclear nuage domains, where amplification is thought to occur. |
| GO:0036464 cytoplasmic ribonucleoprotein granule | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location mapping to cytoplasmic RNP granule, based on PMID:37083324. Reason: Correct but secondary location, as for the IBA above. Supporting Evidence: PMID:37083324 HRDE-1, while predominantly nuclear, also localizes to peri-nuclear nuage domains, where amplification is thought to occur. |
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Download this section (compressed HTML)Q: How does HRDE-1 partition between germ-cell nuclei and perinuclear nuage, and which of its activities (heterochromatin targeting or stimulation of 22G-RNA amplification) is the main driver of transgenerational silencing?
Q: Should siRNA binding be added to HRDE-1 as an experimental annotation (the co-IP and sequencing of 22G siRNAs in PMID:22810588), to replace the inherited miRNA binding IBA?
Experiment: Express a HRDE-1 variant that cannot enter the nucleus, or one held in the nucleus, and measure separately H3K9me3 at target loci and the amount of 22G-RNA amplification over several generations.
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