R-loop mapping of RNA transcripts from bovine papillomavirus type 4.

RNA isolated from bovine oesophageal warts was hybridised to BPV-4 genomic DNA cloned in a plasmid vector. In R-loop preparations, six major classes of transcripts were mapped. Class I, due to an unspliced transcript encompassing the E4/E5 ORF region, is most common. In Class II the E4/E5 region is spliced at its 5' end to the E6 ORF region, and the RNAs appear to have different transcription start points in the E6 ORF. Some Class I R-loops may represent shorter Class II-type transcripts not hybridised to the E6 region. Transcripts that form Class III R-loops have not been previously described for BPV-4 and contain the E4/E5 ORF exon spliced at its 3' end to the LI ORF. In Class IV, transcripts map to the 3' end of the EI exon, artificially truncated by the Bam HI site used for cloning the BPV-4 genome, and are spliced to the 5' end of the exon containing the E4/E5 ORF. Class V transcripts are ambiguously located in the cloned BPV-4 genome, and could be derived from the EI or LI ORF. The former case may represent the remainder of the transcript from Class IV R-loops. The rare Class VI R-loops are due to the L2 ORF spliced at its 3' end to the LI ORF.