SELECTION OF A NONCONSENSUS BRANCH POINT IS INFLUENCED BY AN RNA STEM-LOOP STRUCTURE AND IS IMPORTANT TO CONFER STABILITY TO THE HERPES-SIMPLEX VIRUS 2-KILOBASE LATENCY-ASSOCIATED TRANSCRIPT

Herpes simplex virus ape 1 latent infection in sensory neurons is char acterized by the highly restricted transcription of viral genes. The l atency-associated transcripts (LAT) family members are the only transc ripts that can be identified in large amounts in latently infected cel ls. The most abundant LAT species is a 2-kb RNA that results from spli cing of a rare primary transcript. Analysis of a LAT mutant virus (TB1 ) in cell culture revealed an aberrant splicing pattern and production of a stable small (0.95-kb) LAT intron. A panel of deletion construct s expressing truncated LAT in transiently transfected cells mapped the region influencing stability to the 3' end of the LAT intron. This re gion encompasses the branch point and a putative stable stem-loop hair pin structure immediately upstream of the splice acceptor consensus po lypyrimidine tract. Mutagenic analysis of the sequence in this region confirmed our hypothesis that the stem-loop structure is important for efficient splicing by influencing the selection of a nonconsensus bra nch point. Changes in this structure correlate,vith changes in branch point selection and production of an unstable 2-kb LAT.