In vivo retroviral integration: Fidelity to size of the host DNA duplication might be reduced when integration occurs near sequences homologous to LTR ends

Integrated retroviral DNAs are flanked by a short duplication of target DNA whose size is virus specific and invariable. We have sequenced the junctio ns between an ALSV (Avian Leukemia and sarcoma Viruses)-based Vector and qu ail DNA from five individual proviruses. Three proviruses were flanked by t he expected 6-bp duplication of host DNA, whereas the two others were flank ed by a 5-bp duplication. Nucleotide sequencing of the native integration s ites of these two proviruses showed that these integrations had occurred at the immediate vicinity of either a CA or a TG dinucleotide, revealing stri king microhomologies between the integration sites and Viral LTR ends. Thes e results suggest that size duplication of the target DNA might be influenc ed by nucleotidic sequence at the site of integration. (C) 2000 Academic Pr ess.