Transcriptional analysis of the herpes simplex virus type 1 region containing the TRL/UL junction

In this study we have used a combination of Northern blot, cDNA, and RNAse protection analysis to characterize transcription occurring at the junction of the long terminal repeat (TRL) and long unique segment (UL) of herpes simplex virus type 1 (HSV-1). Two low abundance 5' colinear transcripts mapped between the junction of the TRL/UL and the cap site of the primary latency associated transcripts (LAT). Analysis of the region containing the first four open translational reading frames (ORFs) of the UL segment of the virus revealed a complex pattern of overlapping transcripts and polyadenylation site utilization. Inefficient termination late, but not early in infection, at the polyadenylation site following the UL2 ORF leads to an unusual situation where the promoter controlling a beta gamma transcript encoding the UL1 ORF also controls a 5' colinear gamma transcript. Further, although the entire UL3 ORF is conserved between HSV-1 and HSV-2, the only abundant uniquely UL3 encoding transcript in both virus types was found to originate within the UL3 ORF and has the capacity to encode only a truncated UL3 protein product.