Transposable element targeting by piRNAs in laurasiatherians with distinct transposable elementhistories

Abstract

PIWI proteins and PIWI-interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and posttranscriptional repression of TEs. Most of our understanding of the mechanisms of piRNA-mediated TE silencing comes fromfruit fly andmouse models.However, eveninthese well-studiedanimals it is unclearhowpiRNAresponses relate to variableTE expressionand whether the strength of thepiRNAresponse affects TE content over time.Here,weassessed the evolutionary interactions between TE and piRNAs in a statistical framework using three nonmodel laurasiatherianmammals as a study system:dog, horse, and a vesper bat. These three species diverged ∼80 million years ago and have distinct genomic TE contents. By comparing species with distinct TE landscapes,we aimedto identify clear relationships amongTE content, expression,andpiRNAs.We foundthat the TE subfamilies that are the most transcribed appear to elicit the strongest "ping-pong" response. This was most evident among long interspersed elements, but the relationships between expression and ping-pong pilRNA(piRNA-like) expression were more complex amongSINEs. SINE transcriptswere equally abundant in the dog and horse yet new SINE insertionswere relatively rare in the horse genome,where we identified a stronger piRNA response. Our analyses suggest that the piRNA response can have a strong impact on the TE composition of a genome.However, our results also suggest that the presence of a robust piRNAresponse is apparently not sufficient to stop TE mobilization and accumulation.