Differential selective regimes identify categories of transposable elements with regulatory function

Transposable elements (TEs) are powerful drivers of genome evolution, in part through their ability to rapidly rewire the host regulatory network by creating transcription factor binding sites that can potentially be turned to the host’s advantage in a process called exaptation. We use methods of comparative genomics and population genetics to identify the TE categories that have most contributed to this process. For each TE category, we compare the copies overlapping regulatory elements to all other copies in terms of measures of selection. Using phyloP scores, we find a large number of TE categories showing evidence of conservation specifically when overlapping regulatory elements. The TE categories identified by such analysis are involved in the regulation of gene expression, in the heritability of complex traits, and in specific development-related functions. The same analysis conducted using Tajima’s D, thus exploring more recent selection, shows similar results, although with much lower statistical power. These results suggest that TE categories are heterogeneous in their ability to rewire the human regulatory network in a way that is useful and thus exapted by the host genome; and that the analysis of selective pressure is a powerful tool to identify the TE categories playing the most important roles in gene regulation.