Concurrent sequence analysis of 5′ and 3′ RNA termini by intramolecular circularization reveals 5′ nontemplated bases and 3′ terminal heterogeneity for lymphocytic choriomeningitis virus mRNAs

We have used a technique of RNA circularization coupled with polymerase chain reaction amplification for simultaneous analysis of the 5′ and 3′ termini of subgenomic mRNAs derived from the S RNA of lymphocytic choriomeningitis virus during an acute infection of BHK cells. These mRNAs possess 1 to 7 nontemplated nucleotides of apparently random sequence at their 5′ ends. The predominant mRNA species have 4 or 5 nontemplated nucleotides. The 5′ termini of the mRNAs also have properties consistent with the presence of a 5′ cap structure. The 3′ termini of the mRNAs lack poly(A) tails, and we have shown that transcription termination occurs at heterogeneous positions within the intergenic region of the S RNA. The identification of several distinct termini in the vicinity of a putative stem-loop structure in the RNA templates suggests that transcription termination may be mediated by a structural signal rather than a precise sequence signal.