Transcriptional mapping of the 3' end of the bovine syncytial virus genome

Abstract

The bovine syncytial virus, a member of the retroviral subfamily Spumavirinae, causes a persistent, asymptomatic infection in cattle. Nucleotide sequence analysis of the viral genome revealed two overlapping reading frames in the 3' region, traditionally occupied by accessory-function genes in other complex retroviruses. In order to analyze the transcripts from the accessory-gene region, we designed oligonucleotide primers complementary to sequences within the 5' and 3' long terminal repeats (LTRs) for use with the PCR. Southern blot analysis of amplification products revealed eight major cDNA bands. Eleven distinct cDNA clones were subsequently isolated and characterized. The initial splice donor in each clone is located 49 bp downstream from the mRNA cap site in the 5' LTR. The primary splice acceptor site was located 17 bp upstream from the proximal 3' open reading frame known as BF-ORF1. A second major splice acceptor was localized to a region upstream of the second open reading frame, BF-ORF2. Clones were identified which spliced directly to each of these sites. Additional splice donor and acceptor sites within BF-ORF1 and BF-ORF2 and the 3' LTR were variously used to generate a complex array of multiply spliced transcripts. Each of these transcripts remained in frame and coded for a potential protein product.