Figure 1

CLIP-Seq alignments are enriched and depleted in specific TEs. (A) Across the entire transcriptome (including introns), we counted overlapping aligned reads in the CLIP-Seq and null model simulation for every TE family in both orientations. The top track draws an example gene with blue boxes representing exons. The track below draws a set of example TEs, colored by family and with arrowhead describing orientation. Alignment coverage from CLIP-Seq and null simulation experiments are drawn below, with CLIP-Seq coverage spiking primarily on the purple TE in antisense orientation to the gene. (B) Heatmap in which we plotted the log2 ratio of the CLIP-Seq and null model counts, normalized by library size, for every pair of TE family in both orientations on the y-axis and RBP (with publication first author) on the x-axis. The heatmap was column mean normalized. Black rectangles highlight well-characterized interactions between STAU1 and Alu elements and hnRNP C and antisense Alu elements. TcMar-Tigger and hAT-Charlie are DNA transposons, which transpose via a cut-and-paste mechanism. ERVL, ERV1, and ERVL-MaLR are endogenous retrovirus families that have long terminal repeats (LTRs) on both ends. Both long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) are non-LTR retrotransposons, which mobilize via an RNA intermediate using a copy-and-paste mechanism.