Fig. 2

Model for 5ʹ pA site activation in the HIV genome by MSD-inactivation. a Cartoon of the proposed model for pA site regulation in the HIV RNA genome: suppression of the 5ʹ pA site by the downstream MSD and activation of the 3ʹ pA site by the upstream USE. See the text for further details. The pA hairpins and the upstream TAR hairpins are shown. The pA hairpin structure suppresses both 5ʹ and 3ʹ polyadenylation and allows the MSD/USE control. The 3ʹTAR hairpin juxtaposes the USE and the 3 pA site, which may enhance USE-mediated activation of polyadenylation [14]. The black triangles indicate the position of the AAUAAA polyadenylation signal. The grey arrow represents the actual site of polyadenylation at position 97 (5ʹ copy) or 9229 (3ʹ copy). b Illustrated are the HIV transcripts expected for wild-type MSD⁺ viruses (full-length unspliced and spliced versions, SA is one of the many splice acceptors in the HIV genome) and mutant MSD⁻ proviruses (only short TAR transcripts). (A)n is the polyA tail