Repeat insertion domains of lncRNAs (RIDLs). (A) In the RIDL model, exonically inserted fragments of transposable elements (TEs) contain pre-formed protein-binding (red), RNA-binding (green), or DNA-binding (blue) activities that contribute to the functionality of the host lncRNA (black). RIDLs are likely to be a small minority of exonic TEs, coexisting with large numbers of nonfunctional “passengers” (gray). (B) RIDLs (dark orange arrows) will be distinguished from passenger TEs by signals of selection, including (1) simple enrichment in exons, (2) a preference for residing on a particular strand relative to the host transcript, and (3) elevated evolutionary conservation in exons compared with introns. Selection might be identified by comparing exonic TEs to a neutral population, for example, those residing in lncRNA introns (light-colored arrows).
