Heterogeneity in mRNA of human papillomavirus type-6 subtypes in respiratory tract lesions

We have analyzed the structure of viral transcripts in six HPV-6c-induced respiratory tract lesions, which included four benign laryngeal papilloma, one benign nasopapilloma, and one malignant tumor, in four benign laryngeal papilloma induced by HPV-6e, and in one benign laryngeal papilloma induced by HPV-6f. Northern analysis and S1 nuclease digestion with subgenomic RNA probes demonstrated that the major exon of 1050 bases had a 5' end in the E4 open reading frame and a 3' end in E5B. Primer extension from a synthetic oligonucleotide in E4 was used to examine sequences 5' to the major exon. Differences were found in length, start sites, and relative abundance of the first exon in transcripts produced in HPV-6c-induced infections as compared to HPV-6e- and HPV-6f-induced infections. Primer extension in the presence of dideoxynucleotides facilitated sequence analyses of the first exon. HPV-6c transcripts contained common sequences from E1 that in different transcripts extended farther upstream in the 5' direction into E7 resulting in different lengths. All of the mRNAs had the same splice junction at nucleotide 847 in E1 and 3325 in E4. Similarly, the HPV-6e transcripts shared common sequences in the first exon that differed in length as a result of different starting points and had the same splice junction as the HPV-6c transcripts. No differences were found in the structure of viral transcripts in a malignant vs benign lesions, nor in those of nasopapilloma vs laryngeal papilloma when induced by the same HPV-6 subtype.