Regulation of coronavirus RNA transcription is likely mediated by protein-RNA interactions

Coronavirus mRNA transcription was thought to be regulated by the interaction between the leader RNA and the intergenic (IG) sequence, probably involving direct RNA-RNA interactions between complementary sequences. In this study, we found that a 9-nucleotide sequence immediately downstream of the leader RNA up-regulated mRNA transcription and that a particular strain of mouse hepatitis virus (MHV) lacking this 9-nucleotide transcribed subgenomic mRNA species containing unusually heterogeneous leader-fusion sites. These results suggest that the sequence complementarity between the leader and IG is not necessarily required for mRNA transcription. UV cross-linking experiments using cytoplasmic extracts of uninfected cells and the IG sequence showed that three different cellular proteins bound to IG of the template RNA. Deletion analyses and site-directed mutagenesis of IG further demonstrated a correlation between protein-binding and transcription efficiency, suggesting that these RNA-binding proteins are involved in the regulation of coronavirus mRNA transcription. We propose that coronavirus transcription is regulated by RNA-protein and protein-protein interactions.