Classic template switch mechanism and the new four-point model. (A,B) The classic template switch mechanism creates perfect inverted repeats. (A) DNA replication (blue arrow) exchanges template and converts a nearly perfect inverted repeat (dashed red arrows) into a perfect one (solid red arrows), causing a cluster of differences (bulge, bottom); this can happen by an intra-strand (left) or an inter-strand (right) switch. (B) An inter-strand switch may invert the spacer of the repeat (black dots). (C,D) Our new four-point model generalizes the template switch mutation process while remaining compatible with the classic model proposed by Ripley (1982): C describes both cases of A, and D is consistent with B. Template exchanges are described with four switch points (labeled ①–④) projected onto a reference sequence (R). The points define three sequence fragments (F1–F3) which, when concatenated, create a mutated output. F1 and F3 are copied from R; F2 is copied complementary to either F1 (intra-strand switch) or R (inter-strand switch). (E,F) Examples of mutation clusters compatible with the new model. The template switches (top) can perfectly explain complex mutations observed in real data (bottom; mismatches shown in lower case in the human sequence). (E) Event “3-2-1-4,” named for the order of the switch points along R, creates an inverted repeat (bottom; red arrows) (Link to the original data: http://grch37.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=548;r=11:133333935-133333985). (F) Event “3-1-2-4” creates an inverted repeat (red arrows) separated by an inverted spacer (dotted line) (Link to original data: http://grch37.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=548;r=12:74744810-74744853). (G,H) Predicted secondary structures generated by the inverted repeats created in the human sequences, E and F, respectively.
