Figure 4.

Sequence context among sites of APOBEC3G deamination. (A) The ordinates represent the substitution frequency as a function of the 5′ nucleotide. The dot indicates the deaminated C residue. Deamination in the minus strand occurs preferentially in local sequence context in the order 5′CpC > TpC > ApC ∼ GpC, or on the plus strand 5′GpG > GpA > GpT ∼ GpC. This sequence context is typical for hypermutated genomes derived from Δvif viruses grown on APOBEC3G producing cells (2–6,13). The lightly stippled bars indicate the frequency expected assuming no dinucleotide bias. A χ² analysis showed that for reactions with 2, 3 and 4 µg of APOBEC3G, the observed 5′CpC frequencies proved highly significant (P < 0.001) compared to the expected values. Informative analysis of the 3′ nucleotide context is precluded given that the single CpG target is also a hot spot for deamination. (B) Overall GpG substitution frequencies increase linearly with those in GpA sites.