Contribution of TEs to different gene features of lncRNAs.

A. Schematic of the type of overlap between TE and lncRNA sequences. Upper panel shows an idealized lncRNA transcription unit, and lower panel shows a protein-coding gene (only genes with annotated 5′ and 3′UTRs were analyzed; see Methods). Exons (grey boxes) overlapping a TE are categorized based on the type of overlap: the TE may provide functional feature(s), as a transcription start site (TSS), the first exon (including TSS and splicing site: TSS+SPL), a splicing site (SPL), a middle exon (including the 2 splicing sites (Both SPL), a polyadenylation site (polyA), the last exon (including splicing site and PolyA: PolyA+SPL). A TE not overlapping with any feature is called exonized. B. Comparison between observed (Obs) and random (Rand) distribution (see Methods). Note that a given exon can belong to several categories since a given TE can hit different exons and therefore be counted multiple times. Unhit exons correspond to exons with no TE overlap. Human: lncRNAs from Gencode v13. Mouse: lincRNAs from Ensembl release 70. With the exception of ‘exonized’, ‘TSS’ and ‘polyA’ categories in mouse (p-values = 1, 0.001 and 0.298 respectively) and ‘exonized’ category in zebrafish (p-value = 0.001), the p-values were systematically