Evidence for new transcriptional units encoded at the 3' end of the mouse hepatitis virus genome.

Prior studies have demonstrated that the mouse hepatitis virus (MHV) genome is divided into at least seven coding regions each transcribed into a distinct mRNA. The majority of these mRNAs are synthesized from a highly conserved intergenic start site (UCU/CAAAC), contain a 65-72 nt leader RNA at their 5' end and form a 3' co-terminal nested set. In this study, we have used radiolabeling experiments to demonstrate the presence of a small approximately 900 nt mRNA and its corresponding RF RNA in MHV-infected cells. Surprisingly, PCR amplification and sequence analysis revealed the presence of not one, but two small leader-containing RNAs that initiate from highly conserved intergenic start sites (UCCAAAC and UCUAAAU) which are located within the 3'-most nucleocapsid gene sequence. These studies provide evidence suggesting that one or two additional small mRNAs are encoded from the 3' end of the MHV genome.