Figure 2.

Proposed model for episome formation and integration in cells transduced with polypurine tract (PPT)-positive or PPT-deleted vectors. (a) The RNA genomes of PPT-positive vectors undergo plus-strand synthesis (depicted as a dashed line) initiation at the PPT, leading to efficient strand displacement and producing primarily linear episomes, with a small number of 1-long terminal repeat (LTR) circles formed by failed strand displacement. Linear episomes may then serve as the substrates for homologous recombination (HR), forming 1-LTR circles; nonhomologous end-joining (NHEJ), forming 2-LTR circles; and integrase-mediated integration, forming integrated provirus. (b) The RNA genomes of PPT-deleted (ΔPPT) vectors undergo plus-strand synthesis initiation at cryptic sites upstream or downstream of the PPT, leading to inefficient strand displacement and producing primarily 1-LTR circles (plus-strand synthesis is represented by dashed lines). However, in the few instances in which initiation of plus-strand synthesis from non-PPT sites (from sites located either upstream to the deleted PPT or in the 3′U3) is followed by strand displacement, the aberrant episomal linear forms contained either additions to their 5′ ends or deletions in the 5′ U3 region. NHEJ-mediated circularization of these aberrant linear forms generate 2-LTR circles containing either an insertion between the LTRs or a deletion in the 5′ U3 region. The aberrant linear forms that lack the 5′ integrase attachment (att) site do not support efficient integrase-mediated integration.