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This strategy to generate mutant herpesvirus progeny does not only avoid the remaining of any vector sequences in the viral genome it also reduces the risk of illegitimate events of homologous recombination of the chimeric DNA during the bacterial or viral DNA replication.
This part of the vector should not integrate in the targeted locus following accurate homologous recombination and therefore allows the negative selection of illegitimate events by crossing to a suitable Gal4 driver.
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The majority of break points detected in this study are "clean" break points, where the sequence near the break point shows few differences from the reference, which suggests that these break points are the result of illegitimate recombination events.
Regardless of the molecular mechanism, inhibition of DSB repair in stem cells may result in chromosomal aberrations by either illegitimate recombination events (Bassing and Alt 2004) or reduced functionality of nonhomologous end-joining (Fischer and Meese 2007).
This could facilitate the occurrence of illegitimate recombination events within the LMW-GS genes and result in novel allelic variations, such as chimeric genes [ 9].
This is a common problem previously described in various plant studies (Mazars et al. [1991]) and it is likely caused by illegitimate recombination events that also occur during fungal transformation (Choi et al. [2007]).
In addition, it may cause illegitimate transcription events [17], [18].
Type III products (2/28) appeared to have been generated by reciprocal illegitimate recombination events (Figure 4A (III), Figure S5).
It has also been suggested that phosphorylation of H2AX helps anchor chromosomal ends together, reducing the chances of DSBs leading to illegitimate recombination events [12].
Alternatively, it is possible that cryptic LoxP sites such as those present in mammalian genomes [60] resulted in illegitimate recombination events.
However, this strategy can be associated with illegitimate recombination events during the bacterial or viral DNA replication or it's efficiency can highly depend on the vector insertion site within the viral genome.
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