The length and sequence composition of vesicular stomatitis virus intergenic regions affect mRNA levels and the site of transcript initiation.

In this study, we used a dicistronic vesicular stomatitis virus (VSV) minigenome to investigate the effects of either single or multiple nucleotide insertions placed immediately after the nontranscribed intergenic dinucleotide of the M gene on VSV transcription. Both Northern blot and primer extension analysis showed that the polymerase responded to the inserted nucleotides in a sequence-specific manner such that some insertions had no effect on mRNA synthesis from the downstream G gene, nor on the site of transcript initiation, whereas other insertions resulted in dramatic reductions in transcript accumulation. Some of these transcripts were initiated at the wild-type site, while others initiated within the inserted sequence. We also examined the transcriptional events that occurred when a natural, 21-nucleotide intergenic region located between the G and L genes from the New Jersey (NJ) serotype of VSV was inserted into the minigenome gene junction. In contrast to the normal 25 to 30% attenuation observed for downstream transcription at gene junctions containing the typical dinucleotide (3'-GA-5') intergenic region, the NJ variant showed greater than 75% attenuation at the gene junction. In addition, the polymerase initiated transcription at two major start sites, one of which was located within the intergenic sequence. Collectively, these data suggest that the polymerase "samples" the intergenic sequences following polyadenylation and termination of the upstream transcript by scanning until an appropriate start site is found. One implication of a scanning polymerase is that the polymerase presumably switches states from a processive elongation mode to a stuttering mode for polyadenylation to one in which no transcription occurs, before it reinitiates at the downstream gene. Our data support the hypothesis that sequences surrounding the intergenic region modulate these events such that appropriate amounts of each mRNA are synthesized.