Differences exist between viral transcripts in cottontail rabbit papillomavirus-induced benign and malignant tumors as well as non-virus-producing and virus-producing tumors.

Five major cottontail rabbit papillomavirus-specific polyadenylated RNA species with sizes of 4.8, 2.6, 2.0, 1.3, and 0.9 kilobases (kb) were found in virus-producing tumors of cottontail rabbits (the natural host for the virus). Two of the RNA species (sizes, 2.0 and 1.3 kb) are indistinguishable with respect to size and map position from the RNA species detected previously in non-virus-producing benign and malignant tumors (Nasseri et al., J. Virol. 44:263-268, 1982). The 2.0-kb RNA in virus-producing benign tumors is more abundant than the 1.3-kb RNA. This, together with similar observations of benign non-virus-producing tumors, suggests that the predominance of the 2.0-kb RNA is a general feature of benign tumors. The change to a preferential synthesis of the 1.3-kb RNA appears to be a phenomenon of tumor progression from papillomas to carcinomas. Three transcripts of 4.8, 2.6, and 0.9 kb are unique to virus-producing tumors. The RNA molecules were mapped in two steps. First, hybridization of Northern blots with subgenomic probes revealed the approximate map position of the transcripts. Second, with nuclease S1 and exonuclease VII mapping procedures and end-labeled probes, the major exons of the 4.8-, 2.6-, 2.0-, and 1.3-kb RNAs were mapped precisely, and it is shown that all RNAs are transcribed from the same DNA strand. Both 1.3- and 2.0- kb RNAs consist of two exons which are separated by an identical 2.45-kb intron. The 5' ends of the 5'-proximal exons of the 2.0- and 1.3-kb RNAs map to positions 0.07 and 0.16, respectively. Some of the 2.0-kb RNA molecules, especially in the carcinoma, have an alternative 5' end at position 0.06. The 3' ends of both exons map to position 0.22, where two ends were found about seven nucleotides apart. The sizes of the 5'-proximal exons of the 2.0- and 1.3-kb RNAs are 1.23 and 0.48 kb, respectively. The 1.3- and 2.0-kb RNAs share a common 3'-proximal exon of 0.66 (0.61) kb. This exon has two 5' ends 50 nucleotides apart at map position 0.53 and a 3' end at map position 0.61. Only the 3'-proximal part of the 4.8- and 2.6-kb RNAs have been mapped precisely. Both RNAs share a common 3' end at position 0.99. The 2.6-kb RNA part consists of a single 1.59-kb exon which extends to map position 0.79.(ABSTRACT TRUNCATED AT 400 WORDS)