Fig. 3.

Transcripts of endogenous nuclear RNAi targets are nuclear enriched. (A) smFISH against Cer3/gag, Cer8 and oma-1 in WT (N2) and hrde-1 (23°C F3) adult pachytene germlines. Images show a representative longitudinal section through the gonad core. Note that the Cer3/gag and Cer8 smFISH signals were only present in the nuclei, and absent in the cytoplasm core. The same images without background reduction are in Fig. S5. oma-1 smFISH of an oma-1 deletion mutant strain is shown in Fig. S5 as well. (B) RNA-seq analysis of nuclear and cytoplasmic RNA samples from WT (N2) and hrde-1 mutant adults (23°C F3-4). Whole animals were used, allowing both somatic and germline RNAs to be captured in this analysis. The average nuclear and cytoplasmic RNA expression levels (RPKM, x-axis) and the log2 ratios of nuclear to cytoplasmic RNA level (y-axis) are plotted for all 1-kb regions in the genome. Regions with at least 2-fold difference between nuclear and cytoplasm RNA (P≤0.05) are beige.