EGO-1 is one of four C. elegans cellular RNA-directed RNA polymerases (RdRPs) and the principal RdRP of the germline. Acting with the Dicer-related helicase DRH-3 and the Tudor protein EKL-1, it synthesizes 5'-triphosphorylated, antisense 22G small RNAs from germline mRNA templates. The best-characterized EGO-1 products are the 22G-RNAs loaded into the Argonaute CSR-1, which target thousands of germline-expressed genes and promote holocentric chromosome organization and segregation rather than silencing; EGO-1 also contributes to WAGO-class 22G-RNAs and to robust RNA interference against germline-expressed genes. EGO-1 is enriched in perinuclear germ granules (P granules) and is also found in the nucleus and on mitotic chromosomes. It is required for H3K9me2 enrichment on unpaired chromosomes during meiosis (meiotic silencing). Loss of ego-1 causes sterility with pleiotropic germline defects in proliferation, meiosis, gametogenesis, nuclear pore and P-granule organization.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000794 condensed nuclear chromosome | IDA PMID:19804758 The Argonaute CSR-1 and its 22G-RNA cofactors are required f... | KEEP AS NON CORE | Summary: EGO-1, together with CSR-1, DRH-3 and EKL-1, was shown by immunostaining to associate with chromosomes in embryonic cells (PMID:19804758). Reason: Direct localization evidence from the curators' source; the chromosome association reflects the CSR-1 22G-RNA pathway acting at chromatin during mitosis. It is a real but secondary location relative to the perinuclear germ granules where most germline EGO-1 is seen (PMID:21396820). Supporting Evidence: PMID:19804758 the RNA-dependent RNA polymerase EGO-1, the Dicer-related helicase DRH-3, and the Tudor-domain protein EKL-1 localize to chromosomes and are required for proper chromosome segregation PMID:21396820 in adult germline tissue, where EGO-1 function is essential, EGO-1 staining is not evident on chromosomes |
| GO:0001172 RNA-templated transcription | IEA GO_REF:0000108 | ACCEPT | Summary: Inter-ontology IEA from the RdRP activity annotation. RNA-templated transcription is the process realized by RdRP activity. Reason: EGO-1 produces triphosphorylated antisense small RNAs from mRNA templates (PMID:21396820), which is RNA-templated RNA synthesis. The term is a consistent logical consequence of the MF. Supporting Evidence: PMID:21396820 Our data support the conclusion that EGO-1 produces triphosphorylated small RNAs derived from mRNA templates |
| GO:0003968 RNA-directed RNA polymerase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for RdRP activity in the eukaryotic RdRP family (PTN000554964), with RRF-1 (WBGene00004508), S. pombe Rdp1 and Arabidopsis RDR among the descendant evidence. Reason: EGO-1 is a full-length member of the cellular RdRP family (RdRP domain IPR007855) and in vivo it is required for a distinct pool of 5'-triphosphorylated antisense small RNAs whose structure indicates de novo RdRP synthesis (PMID:21396820). EGO-1 sits squarely within the clade that inherited RdRP activity; there is no evidence of loss. Supporting Evidence: PMID:21396820 EGO-1 is required to produce a distinct pool of small RNAs antisense to a number of germline-expressed mRNAs PMID:10704412 The predicted EGO-1 protein was found to be related to the tomato RNA-directed RNA polymerase (RdRP) and to Neurospora crassa QDE-1 |
| GO:0003968 RNA-directed RNA polymerase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro IPR007855 RdRP domain; EC 2.7.7.48). Reason: Consistent with the IBA and with in vivo small-RNA evidence (PMID:21396820). Supporting Evidence: PMID:21396820 EGO-1 produces triphosphorylated small RNAs derived from mRNA templates |
| GO:0005634 nucleus | IDA PMID:16271877 EGO-1, a putative RNA-dependent RNA polymerase, is required ... | ACCEPT | Summary: Nuclear fractionation and western blotting found most cellular EGO-1 in the nuclear extract (PMID:16271877). Reason: Direct experimental localization, consistent with EGO-1's requirement for H3K9me2 enrichment on unpaired meiotic chromosomes and with chromosome association (PMID:16271877, PMID:19804758). Supporting Evidence: PMID:16271877 Most of the total cellular EGO-1 protein was detected in the nuclear extract, as would be expected if EGO-1 directly interacts with chromatin |
| GO:0005634 nucleus | IDA PMID:19804758 The Argonaute CSR-1 and its 22G-RNA cofactors are required f... | ACCEPT | Summary: Immunostaining localized EGO-1 to chromosomes, i.e. within the nucleus (PMID:19804758). Reason: Consistent with independent fractionation data (PMID:16271877). Supporting Evidence: PMID:19804758 localize to chromosomes and are required for proper chromosome segregation |
| GO:0005737 cytoplasm | IDA PMID:19804758 The Argonaute CSR-1 and its 22G-RNA cofactors are required f... | ACCEPT | Summary: EGO-1 is detected in the germline cytoplasm, concentrated in perinuclear granules (PMID:19804758). Reason: Germline EGO-1 is chiefly perinuclear-granule associated, which is cytoplasmic (PMID:21396820). The more specific P granule annotation is also present. Supporting Evidence: PMID:21396820 antibody staining of adult germline tissue suggests EGO-1 associates with perinuclear RNA-containing granules |
| GO:0007281 germ cell development | IGI PMID:8647392 Enhancers of glp-1, a gene required for cell-signaling in Ca... | KEEP AS NON CORE | Summary: ego-1 was isolated as an enhancer of a weak glp-1 allele and is required for multiple aspects of germline development (PMID:8647392). Reason: The germline developmental requirement is robust but downstream: EGO-1 produces small RNAs that regulate germline gene expression (PMID:21396820). The developmental process is a pleiotropic consequence of its RdRP role. Supporting Evidence: PMID:8647392 Based on genetic experiments, glp-1 appears to act upstream of ego-1 and ego-3. PMID:15911573 EGO-1 acts in parallel with GLP-1 signaling to influence the proliferation vs. meiosis fate choice |
| GO:0007283 spermatogenesis | IMP PMID:10704412 EGO-1 is related to RNA-directed RNA polymerase and function... | KEEP AS NON CORE | Summary: Putative null ego-1 mutants have multiple germline defects including in gametogenesis (PMID:10704412). Reason: Mutant phenotype evidence; gametogenesis defects are pleiotropic downstream consequences of loss of germline 22G-RNA production. Supporting Evidence: PMID:10704412 Putative ego-1 null mutants had multiple, previously unreported defects in germ-line development. |
| GO:0030422 siRNA processing | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA: siRNA processing for the eukaryotic RdRP family (PTN000554964). The GO definition explicitly includes amplification of siRNA by RdRP. Reason: EGO-1 synthesizes germline 22G-RNAs (CSR-1 class and part of the WAGO class) that are made by RdRP complexes with DRH-3 (PMID:19800275, PMID:21396820). This is the core process of the gene. Supporting Evidence: PMID:19800275 DRH-3 is a core component of RNA-dependent RNA polymerase (RdRP) complexes essential for several distinct 22G-RNA systems. PMID:32499657 Thus, EGO-1 may also produce some 22G siRNAs via a pUG RNA-independent mechanism. |
| GO:0031380 nuclear RNA-directed RNA polymerase complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from S. pombe Rdp1 (RDRC). The term is defined as the RdRP complex required for RNAi-mediated heterochromatin assembly. Reason: EGO-1 acts in an RdRP complex with DRH-3 (the Dicer-related helicase that parallels the Hrr1 helicase of S. pombe RDRC) and EKL-1 (PMID:19800275). EGO-1 is mostly nuclear in fractionation and is the only C. elegans RdRP needed for H3K9me2 enrichment on unpaired meiotic chromosomes (PMID:16271877), matching the heterochromatin-assembly role in the term definition. Supporting Evidence: PMID:16271877 Among C. elegans RdRPs, we find that only EGO-1 is required for H3K9me2 enrichment on unpaired chromosomal regions during meiosis. PMID:19800275 DRH-3 is a core component of RNA-dependent RNA polymerase (RdRP) complexes |
| GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing | IMP PMID:10704412 EGO-1 is related to RNA-directed RNA polymerase and function... | ACCEPT | Summary: ego-1 mutants are resistant to RNAi against several germline-expressed genes (PMID:10704412). Reason: EGO-1 performs the secondary-siRNA synthesis step of germline RNAi, so it does part of the work of this silencing pathway (PMID:10704412, PMID:21396820). Supporting Evidence: PMID:10704412 For a number of germ-line-expressed genes, ego-1 mutants were resistant to a form of PTGS called RNA interference. PMID:21396820 we show a strong association between the loss of small RNAs and the rise of mRNA levels in ego-1(-) animals |
| GO:0043186 P granule | IDA PMID:19804758 The Argonaute CSR-1 and its 22G-RNA cofactors are required f... | ACCEPT | Summary: EGO-1 localizes to perinuclear P granules in the adult germline (PMID:19804758). Reason: Germline EGO-1 is concentrated in perinuclear germ granules; this is the main site of the CSR-1 22G-RNA pathway (PMID:21396820, which cites this work). Supporting Evidence: PMID:21396820 antibody staining of adult germline tissue suggests EGO-1 associates with perinuclear RNA-containing granules |
| GO:0048477 oogenesis | IMP PMID:10704412 EGO-1 is related to RNA-directed RNA polymerase and function... | KEEP AS NON CORE | Summary: ego-1 was originally shown to be required for oogenesis; null mutants have multiple germline defects (PMID:10704412). Reason: Pleiotropic germline phenotype; downstream of the RdRP function. Supporting Evidence: PMID:10704412 The ego-1 gene was originally identified on the basis of genetic interactions with the receptor in this pathway and was also shown to be required for oogenesis. |
| GO:0051664 nuclear pore localization | IMP PMID:15911573 EGO-1, a putative RNA-directed RNA polymerase, promotes germ... | MARK AS OVER ANNOTATED | Summary: In ego-1 mutants the size and distribution of germline nuclear pore complexes are altered (PMID:15911573). Reason: The mutant phenotype is real, but EGO-1 is an RdRP and there is no evidence that it acts on nuclear pores. Small-RNA profiling later showed that EGO-1 targets include nuclear pore assembly genes, whose mRNAs rise in ego-1 mutants (PMID:21396820). The NPC defect is therefore most likely an indirect consequence of misregulated gene expression, not EGO-1 participation in nuclear pore localization. Supporting Evidence: PMID:15911573 the size and distribution of nuclear pore complexes and perinuclear P granules are altered in the absence of EGO-1 PMID:21396820 These potential mRNA targets fall into distinct classes, including genes required for kinetochore and nuclear pore assembly |
| GO:0070090 metaphase plate | IDA PMID:19804758 The Argonaute CSR-1 and its 22G-RNA cofactors are required f... | KEEP AS NON CORE | Summary: Claycomb et al. showed EGO-1 on mitotic chromosomes, which in mutants fail to align at the metaphase plate (PMID:19804758). Reason: Consistent with the chromosome localization; a mitotic sub-location that is secondary to EGO-1's germline granule and nuclear localizations. Supporting Evidence: PMID:19804758 In the absence of these factors chromosomes fail to align at the metaphase plate |
| GO:1903863 P granule assembly | IMP PMID:28182654 ELLI-1, a novel germline protein, modulates RNAi activity an... | MARK AS OVER ANNOTATED | Summary: ego-1 alleles recovered in a screen for P-granule defects have P-granule phenotypes like csr-1, ekl-1 and drh-3 mutants (PMID:28182654). Reason: The phenotype is shared by all CSR-1 pathway mutants. EGO-1 is an RdRP, not a granule scaffold, and P-granule changes in ego-1 mutants accompany broad germline defects (PMID:15911573). No evidence shows EGO-1 doing part of the work of granule assembly, so the annotation reflects an indirect effect. Supporting Evidence: PMID:28182654 Similarities between the P-granule phenotypes of csr-1, ego-1, ekl-1, drh-3 and elli-1 suggests ELLI-1 functions with or in parallel to CSR-1 |
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Download this section (compressed HTML)Q: Recombinant or immunopurified EGO-1 has not clearly been shown to have RdRP activity in vitro, unlike RRF-1. Does EGO-1 show primer-independent RdRP activity, and does it use pUG-tailed templates as RRF-1 does?
Q: What determines which templates go to EGO-1 (CSR-1 class) and which to RRF-1 (Mutator/WAGO class), given that both are germline RdRPs and partly redundant for WAGO 22G-RNAs?
Experiment: In vitro RdRP assays with EGO-1 complexes immunopurified from germline extracts, using a catalytic-site (DxDxD) mutant as control.
Hypothesis: EGO-1 has intrinsic, primer-independent RdRP activity that produces 22-nt 5'-triphosphorylated products.
ego-1 encodes a homolog of RNA-directed RNA polymerase; ego-1 is essential for several aspects of germline development such as proliferation, heterochromatin assembly on unpaired DNA during meiosis, and gametogenesis; ego-1 is also required for RNAi in the germ line; EGO-1 is detected in nuclear extracts.
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