Fig. 4: Endogenous mRNAs regulated by RDE-1.
From: ER-associated RNA silencing promotes ER quality control
a, Fluorescence images of mutant worms for the exo-RNAi pathway expressing ATM. Pharyngeal expression of Pmyo-2::mCherry serves as transgenic marker. Scale bar, 200 µm. b, Quantification of GFP fluorescence intensity of ATM expressing worms together with rde-1(ne219) mutation. Measurements were carried out with the BioSorter using at least 200 animals per replicate, which were merged and displayed in ridgeline density plots. c, α-Amanitin chase assays for ATM mRNA from rde-1(ne219) mutants expressing ATM. mRNA measured by qRT–PCR. d, RNA sequencing results of cpl-1*-expressing worms bearing the rde-1(ne219) mutation or the WT allele. Cut-off for upregulated constructs: P ≤ 0.05. e, A total of 485 transcripts identified in d were subjected to BUSCA subcellular localization analysis. f, Subcellular component GO term enrichment for the genes identified in d and e. g–j, α-Amanitin chase assays for indicated endogenous mRNAs identified in d from rde-1(ne219) mutants and WT animals expressing cpl-1*. mRNA measured by qRT–PCR. k,l, Endogenous rol-6, sqt-1 (k) and pas-7 (l) mRNA level measured by qRT–PCR in vehicle (DMSO)- versus tunicamycin-treated WT worms. Data relative to 18S rRNA. m, α-Amanitin chase assays for endogenous cpl-1 mRNA from ATM expressing animals with the rde-1(ne219) mutation or WT allele. mRNA measured by qRT–PCR. In c, g–j and m, data are relative to cdc-42 and pmp-3 mRNA. In b, data were analysed by pairwise t-test with Holmes multiple comparison test. In k and l, data were analysed by one-way ANOVA with Sidak’s multiple comparison test. In c, g–j and m, data were analysed by two-way ANOVA with Dunnett’s multiple comparison test. Values are depicted as mean ± s.e.m or, in c and g–m, as mean (white circles) ± standard deviation (s.d.) (white error bars). Data in b are generated from n = 3 independent experiments. *P < 0.05; **P < 0.01; ***P < 0.001; NS, P > 0.05. In f, raw P values were corrected for FDR. *FDR <0.05; **FDR <0.01; *** FDR <0.001; NS, FDR >0.05. Source numerical data are available in source data.
