Fig. 6: Twin mutation hotspot combining optimal TpC and VpC sites.

A twin mutation hotspot detected in the gene PLEKHS1 contains an optimal hairpin substrate on each strand of the DNA. A On one DNA strand, the hairpin contains the sequence GAAC, and the C in last position is an optimal VpC substrate for A3A. B On the other DNA strand, the hairpin contains the sequence GTTC, and the C in last position is an optimal TpC substrate for A3A. However, when A3A generates a mutation at either strand’s site, and the cell goes through DNA replication, then the mutation becomes propagated to the complementary strand, in the first (5’) position of the loop. This mutation causes the local sequence context to no longer be optimal, leading to a decrease in the observed mutation frequency in tumors (bar plots). Error bars represent 95% confidence intervals. C In vitro APOBEC3A assay confirms activity at GAAC hairpin loop sequence. Changing to AAAC or CAAC reduces the substrate optimality by corrupting the optimal GAAC sequence. Source data are provided as a Source Data file.