Mapping of Low Abundance Latency-associated RNA in the Trigeminal Ganglia of Mice Latently Infected with Herpes Simplex Virus Type 1

During herpes simplex virus type 1 (HSV-1) latent infection of the mouse trigeminal ganglion there is limited viral gene expression. The latency-associated transcripts (LAT) map approximately to the PstI-MluI fragment within the BamHI B and BamHI E fragments (long repeat regions) of the viral genome. Additional weak hybridization signals have been detected by in situ hybridization that correspond to transcription from HSV-1 DNA fragments adjacent tot he PstI-MluI fragment. We mapped the region encoding this additional transcription. This minor latency-associated RNA (m-LAT) was shown to map to a group of contiguous fragments (approximately 8.3 kb of DNA), which are adjacent to the 3' end of LAT and to a (2.0 kb) fragment adjacent to the 5' end of the LAT. Using single-stranded probes in in situ hybridization experiments, we showed that the KpnI-BamHI and BamHI-SacI regions of m-LAT are transcribed in a rightward direction within the long internal repeat region. This low abundance RNA may be related to the previously described LAT.