In the manuscript, we discuss the importance of the ORF2 protein slippage in the maintenance of active SINE source elements in primate lineages. This property of the ORF2 protein has several implications on mobile element biology. However, one of the most interesting observations was the consistent expansion of the A-tail of de novo inserts due to slippage of the LINE-1 ORF2 protein during reverse transcription. Analysis of the distribution of de novo inserts also reinforced their mutagenic potential, with new Alu elements showing an insertional preference into genes and other SINEs. This was particularly surprising to us, as the tissue culture assay system requires the dramatic change of the length of the 300 bp Alu transcript through the addition a sequence tag of almost 2000 bases. For example, the features of the recovered Alu inserts were highly consistent with the observed characteristics of genomic Alu elements, validating the assay system as a useful tool to study SINEs. This is a valuable system that provides a complementary approach to genomic analysis.
In Wagstaff et al., 1 we described our findings using an adaptation of a tagged Alu system that would allow for the recovery of over 200 de novo Alu inserts in culture.
