Fine mapping of the major latency-related RNA of herpes simplex virus type 1 in humans.

In situ hybridization with synthetic oligonucleotides was used to fine map the extent and continuity of herpes simplex virus type 1 (HSV-1) latency-related RNA (LR RNA) in trigeminal ganglia of latently infected humans. A series of 34 20 residue oligonucleotides were employed to cover a 3 kb region of the HSV-1 genome to which the latency-related gene had previously been mapped. The 5' end of the main LR RNA transcript began approximately 1210 nucleotides downstream from the 3' end of the mRNA from the immediate early gene ICP0. The 3' end of the LR RNA overlapped the 3' end of the ICP0 mRNA by approximately 1000 nucleotides. A potential small intron was detected near the 3' end of the LR RNA.