TABLE 1.
Levels of representative small RNAs detected by Northern blot analysis of total RNA from strains defective in components of RNAi pathways
| Small RNA levelsb | |||||||
|---|---|---|---|---|---|---|---|
| Genotype | Gene producta | RNAi functiona | siRNAc | tncRNAd | miRNA precursore | mature miRNAe | Effects on endogenous RNAif |
| aPreviously published roles in silencing phenomena in C. elegans (Ketting et al. 1999; Tabara et al. 1999; Dernburg et al. 2000; Grishok et al. 2000; Ketting and Plasterk 2000; Bernstein et al. 2001; Grishok et al. 2001; Ketting et al. 2001; Timmons et al. 2001; Simmer et al. 2002; Tabara et al. 2002; Tijsterman et al. 2002a; Kennedy et al. 2004; Chen et al. 2005; Tops et al. 2005). (ex) Exogenous RNAi of germline and somatic genes, (exgl) exogenous RNAi of germline genes preferentially, (exsom) exogenous RNAi of somatic genes preferentially, (eri) enhanced RNAi, (tr) transposon silencing, (co) cosuppression, (mir) microRNA biogenesis and function. | |||||||
| bDetermined by Northern blot as described in Figure 1 and in Materials and Methods; PhosphorImager signals were normalized to U6 levels in each sample and then expressed relative to the wild type. Values in boldface type are those at least fivefold elevated or decreased compared with the wild type. This quantitative cutoff was chosen to capture a subjective judgment of significantly abnormal signals. | |||||||
| cMeasurement shown is for Ct1189; similar results were obtained for Ct1182 (except that only Ct1189 was assayed in eri-1 total RNA). | |||||||
| dMeasurement shown is for tncR35; similar results were obtained for tncR36 and for tncR4 (except that tncR36 and tncR4 were not assayed in eri-1). | |||||||
| eMeasurement shown is for mir-238; similar results were obtained for mir-38, mir-42, mir-52, mir-58, mir-71, mir-79, and mir-229 (except that only mir-238 was assayed in eri-1 total RNA). | |||||||
| fBased on interpretation of results presented in this paper. | |||||||
| gBased on accumulation of pre-miRNA (Figure 1). | |||||||
| hSmall RNAs reduced significantly, as indicated by the data in Figure 1 (and summarized in this table). | |||||||
| iEndogenous messenger RNA elevated, as indicated by the data in Figure 2. | |||||||
| jEndogenous messenger RNAs elevated, as indicated by the data in Figure 3 and Supplemental Table S1. | |||||||
| Wild type | 1.0 | 1.0 | 1.0 | 1.0 | |||
| alg-1(RNAi); alg-2(ok304) | Argonaute | mir | 0.8 | 1.2 | 17 | 0.5 | microRNAsg |
| dcr-1(ok247) | Nuclease | mir, ex, co, tr | 0.1 | 0.7 | 44 | 1.6 | microRNAsg endo-siRNAh |
| rde-1(ne300) | Argonaute | ex | 0.8 | 0.8 | 1.5 | 1.0 | |
| rde-4(ne337) | dsRNA binding | ex | 0 | 0 | 2.7 | 1.7 | endo-siRNAh tncRNAh |
| rde-3(ne298) | Nucleotidyl-transferase | ex, co, tr | 0.1 | 0 | 1.5 | 2.0 | endo-siRNAh tncRNAh mRNA repressioni,j |
| rde-3(r459) | 0 | 0.3 | 0.5 | 0.7 | endo-siRNAh | ||
| rde-2(ne221) | Novel | exgl, co, tr | 0.2 | 0 | 0.4 | 1.3 | endo-siRNAh tncRNAh mRNA repressioni |
| mut-7(pk204) | RNAse D | exgl, co, tr | 0.2 | 0.1 | 3.7 | 1.8 | endo-siRNAh tncRNAh mRNA repressioni |
| mut-14(pk738) | RNA helicase | exgl, tr | 0.1 | 0.3 | 0.5 | 1.6 | endo-siRNAh mRNA repressioni |
| rrf-1(pk1417) | RdRp | exsom | 0.6 | 0.1 | 0.8 | 2.5 | tncRNAh mRNA repressionj |
| rrf-3(pk1426) | RdRp | eri | 0.1 | 0 | 2.3 | 1.9 | endo-siRNAh tncRNAh mRNA repressionj |
| eri-1(mg366) | Exonuclease | eri | 0.2 | 0 | 4.9 | 2.4 | endo-siRNAh tncRNAh mRNA repressionj |
| rrf-2(ok210) | RdRp | unknown | 0.6 | 0.7 | 4.7 | 2.6 | |
