FIG. 6.

Diagrammatic representation of a template-switching model explaining the silencing of homologous recombination hot spots by GC-rich sequences. (A) According to the model, template switching of the BMV replicase (represented by large shadowed double ellipses) occurs during positive-strand (represented by broken lines) synthesis when the replicase pauses at or near the AU-rich portion (represented by a curved line) present on the primary template RNA3 (21). Although partially double-stranded replication intermediates (RIs) are shown, the existence of single-stranded RNAs with negative polarity is also possible (not shown). (B) The released 3′ end of the nascent strand hybridizes to the acceptor strand; this hybridization is facilitated by the temporary formation of bubble structures (non-base-paired regions) within the AU-rich portion of the RI form of acceptor RNA2 (21). The resumption of chain elongation by the BMV replicase is indicated by a rightward-pointing arrow. When GC-rich sequences are present (indicated by a lock on the right), the formation of appropriate bubble structures within the AU-rich portion may be less favored (indicated by smaller loops), thus resulting in a reduced frequency of homologous recombination. It is also possible that the BMV replicase has to enlarge the bubble structures of the RIs during and/or after the docking event on the acceptor RNA. This step can be inefficient if the downstream portions of the RIs are very stable due to their high G+C content. This stability can inhibit successful docking or reinitiation events by the replicase, resulting in a reduced incidence of recombination (see also Discussion and reference 21).