Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in dsRNA Response

Sneha Rath; Eliza Prangley; Jesse Donovan; Kaitlin Demarest; Yigal Meir; Ned Wingreen; Alexei Korennykh

To de novo identify the cleavage sites in human rRNA, we adapted RtcB RNAseq suitable for single-nucleotide resolution mapping . RtcB RNAseq analysis of rRNA from cells with activated 2-5AMD ( Fig. S3A ) revealed cleavage sites with a UN^N consensus (Fig. 3A ) that distinguishes the sequence-specific activity of RNase L (Table S2 ) Han et al., 2014) . We analyzed the data to identify predominant sites that simultaneously exhibit induction and high read count in the 2-5AMD sample, as shown in Figure 3A . A single high-scoring site 771 was detected in 18S rRNA and two dominant sites, 1056 and 4032, were detected in 28S rRNA. Our analysis detected both 28S rRNA sites 4031 and 4032 identified previously by primer extension assay (Iordanov et al., 2000) , providing important validation for the RtcB RNA-seq approach. The dominant sites 771 (18S) and 1056 (28S) were detected for the first time.