Analysis of a 5' leader sequence on murine leukemia virus 21S RNA: heteroduplex mapping with long reverse transcriptase products.

The majority of the mRNA that specifies retrovirus glycoproteins is known to be derived from the 3' half of the genome. To examine whether the glycoprotein mRNA of murine leukemia viruses (MuLVs) might consist of portions derived from both the 5' and 3' ends of the viral genome, we performed hybridization with a 5'-specific probe and heteroduplex analysis with long reverse transcribed DNA. A 5' probe was made by purifying a discrete 50 nucleotide-long reverse transcript attached to its tRNA primer. This probe was found to hybridize to RNA of the size of glycoprotein mRNA--21S, poly(A)-containing RNA--indicating that the mRNA could have a 5' leader sequence. The 5'-specific sequences were studied by electron microscopic examination of hybrids between 21S RNA and the two longest discrete cDNA species synthesized in the endogenous reverse transcriptase reaction. One of these species, 8.8 kb long, is only made in the absence of actinomycin D, but it does not contain any self-complementary sequences, and therefore appears to be a complete transcript of the viral genome. The shorter of the two species, 8.2 kb long, is synthesized whether or not actinomycin D is present; it must terminate 500--600 nucleotides internal to the 5' end of the template RNA. The structures observed in heteroduplexes of 21S RNA and these DNAs indicated the presence of a leader sequence approximately 500 nucleotides long at the 5' end of the 21S RNA. Sequences comprising this leader segment in the 21S RNA mapped at the 5' end of the genome RNA; the rest of the 21S RNA consisted of sequences from the 3' portion of the genome. Analysis of heteroduplexes with 8.2 kb DNA suggested that actinomycin D could block the reverse transcription of most of the sequence in the genome RNA that appears as a leader in the 21S RNA.