Background The HPV-16 virus is well described as a causative agent in cervical cancer.

Aims To individually analyse the transcription profile of the HPV-16 viral genes in patient biopsies of varying grades of cervical dysplasia by a chromogenic in situ hybridisation technique.

Methods 19 formalin fixed, paraffin embedded (FFPE) biopsies of cervical dysplasia were analysed by a chromogenic in situ hybridisation protocol using novel long single stranded digoxigenin labelled DNA probes targeted to the individual HPV-16 gene RNAs.

Results A transcription pattern for all the HPV-16 genes that is always conserved to the upper intermediate and superficial layers of the cervical epithelium and is independent of the level of dysplasia is described. E1 and E6 transcripts were found to express with a uniquely nuclear localisation; all other transcripts had both nuclear and cytoplasmic localisation. E5 oncogene transcripts were abundant in all cases, being equal to or greater than E7. Deep investigation of the E2 RNA transcript showed a potential alternative transcript with a possible novel start codon.

Conclusions This data represents new information on HPV-16 viral transcription events that bring into question some of the current beliefs on the mechanism of HPV-16 infection in the progression to cervical cancer. Results support high expression of the E5 and E7 oncogenes in cervical dysplasias infected by HPV-16 in contrast to the low levels identified for the E6 oncogene and a possible alternative transcript for the E2 gene. The diagnostic utility of the detection of HPV-16 RNA transcripts is becoming more apparent and a renewed look at their in situ localisation in cervical biopsies could be beneficial.