Physiologic RNA targets and refined sequence specificity of coronavirus EndoU

Endoribonuclease cleavage in host and viral RNAs. (A,B) Relative amounts of endonucleolytic cleavage in host and viral RNAs. Normalized cyclic phosphate cDNA reads (reads at each position/total reads in library) mapped to host and viral RNAs at 9 and 12 hpi in wt, IFNAR^−/−, and RNase L^−/− bone marrow macrophages (BMMs). (C) Frequency and location of cleavage sites in MHV RNA. Normalized cyclic phosphate cDNA reads captured at each position along the MHV genomic RNA at 9 and 12 hpi from MHV^(S)-, MHV^(V)-, PDE^mut-, and EndoU^mut-infected wt BMM. Putative cleavage sites attributed to EndoU or RNase L were calculated from RNase L– or EndoU-dependent signal generated by subtracting signal from each captured position that occurs in the absence of either enzyme (RNase L^−/− BMM or during EndoU^mut infection). These data were then filtered for sites with reads representing at least 0.01% of total reads in the library. At each of these positions, the log₂-fold change in signal when either RNase L or EndoU were absent was calculated and sites with ≥2.5-fold change were designated putative RNase L or EndoU sites.