Oligoadenylated 3′ decay intermediates are present in cytoplasmic RNA. Transcription of the Hsp70 reporter was induced for 60 min before cytoplasmic and nuclear RNA was isolated as described in Materials and Methods. (A) The RNA was analyzed by Northern blotting with a reporter-specific probe and probes for U4 and 7SL RNA as markers for the nuclear and cytoplasmic fraction, respectively. The degree of enrichment was calculated from a comparison to additional lanes on the same Northern blot in which total RNA prepared from the same batch of cells was analyzed for U4 and 7SL RNA. (B) Sequencing libraries were generated from the same samples and analyzed by Illumina deep sequencing. Data represent between 1.3 and 2.9 million reads per sample and are averaged from the two independent experiments. The analysis of total RNA from the same cell sample is presented as “not treated” in Figure 2D.
