Thus, following genotoxic stress, Hmo1 facilitates the usage of the Rad5 pathway, promoting template switching accompanied by SCJ formation early in S phase.
Long regions of sequence homology promote template switching during both RT and PCR (Judo et al., 1998; Houseley and Tollervey, 2010); this can generate novel isoforms not originally present in the biological sample.
By analogy, in case of replication in the presence of genotoxic stress, we speculate that topological constrains arising during replication may facilitate annealing of the gap-containing region to the homologous sister duplex and promote template switching (Fig 6, I).
Both the overall length of the RT-PCR products and the extensive region of similar sequence identity in the middle that can promote template switching (see below) confound RT-PCR analysis of the six possible EDA and V exon combinations.
In addition to the model proposed above, and not mutually exclusive, Hmo1 may promote template switching and SCJ formation via its reported ability to induce formation of chromatin loops via DNA-bending (Xiao et al, 2010).
One alternate group of methods to recombine genes are fragmentation-free PCR-based protocols, which utilize a series of short annealing/extension steps to promote template switching, which in turn, leads to recombination.
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