Occurrence of partial deletion and substitution of the src gene in the RNA genome of avian sarcoma virus

The genome size of 20 transformation-defective (td ) viruses derived from different strains of Rous sarcoma viruses [Prague (subgroups A and C), Schmidt-Ruppin (subgroups A and D) (SR-D), Bratislava 77, and Carr-Zilber subgroup D)] was examined by polyacrylamide gel electrophoresis. All of thetd viruses excepttd SR-D have 35S RNA of the same size—i.e., classb RNA. Two of fivetd SR-D viruses examined have a slightly larger RNA, corresponding to atd deletion that is about 25% smaller than that of classb RNA. However, the RNase T1 -oligonucleotide fingerprints of all thetd SR-D viruses are identical, lacking two sarcoma-specific oligonucleotides. The fingerprints of these viruses also showed a minor oligonucleotide present at very low concentration. A study of heteroduplex molecules formed between genome-length cDNA made from wild-type SR-D and 35S RNA oftd SR-D showed a deletion loop of 2.0 and 1.5 kilobases, respectively, at the map position of thesrc gene for these two classes oftd SR-D viruses, confirming the results of polyacrylamide gel electrophoresis. In addition, some heteroduplex molecules with a substitution loop of 0.6-0.7 kilobase at the same site as the deletion loop were observed in all five of thetd SR-D viruses. We conclude that some of thetd SR-D viruses have a partially deletedsrc gene and that all of thetd SR-D viruses have incorporated heterologous sequences of distinct length in some RNA molecules at the position of thesrc gene. The nature and origin of these heterologous sequences are discussed.