Small RNA-Transposable Elements Interactions in Animal Genome Evolution

Transposable elements (TEs) are major factors in determining the size of eukaryotic genomes.  The proliferation of TEs is generally considered deleterious and certain small RNA classes have evolved to protect genomes against TE invasion.  Conversely, TEs also act to introduce potentially valuable genomic variation, encouraging adaptation.  We have been exploring the interaction between TEs and small RNAs within the context of model and non-model taxa from both standpoints.  From the latter standpoint, we have found that TEs are a major source of microRNAs (miRNAs) in bats.  Furthermore, the deposition of those miRNAs coincide with the diversification of the largest family of bats, suggesting that TEs can act as major players in the generation of species diversity  From the former standpoint, we have found that the genomic abundance of new TEs does not always match the abundance of TE transcripts, resulting in speculation that a strong piRNA response in horses could explain a near zero rate of recent SINE accumulation whereas a relatively relaxed post-transcriptional SINE silencing response of piRNAs in dogs genome might account for the substantially higher SINE insertion rate. This observation suggests that differences in the PIWI/piRNA response to TE challenges can have substantial impacts on genomic TE content.