Fig. 4: TE splicing patterns and frequencies of TE-containing coding and noncoding transcripts.

a The splicing patterns of different TEs in coding transcripts. Coding transcripts were divided into 5’ UTR, CDS and 3’ UTR, and scaled to a uniform size. UTR=untranslated region; CDS=coding sequence. b Proportion of TEs 2 kbp upstream and downstream of coding transcript TSS (transcription start site) and TES (transcription end site). c Proportion of TEs around 200 bp upstream and downstream of the donor and acceptor splice sites of coding transcripts. d The splicing patterns of different TE superfamilies in noncoding transcripts. Each transcript is scaled to a uniform size. e TE contents around the TSS and TES of noncoding transcripts. f TE content around the donor and acceptor sites in the noncoding transcripts. The TE content for each bin was then computed. g Heatmap of TEs with significant differences in coding transcript frequencies between hPSCs and any of the three cell types. h Heatmap of TEs with significant frequency differences in the noncoding transcripts of the hPSC and any of the three cell types. For g and h the statistical significance was defined as an adjusted P value < 0.05 and odds ratio ≥2 from a Fisher exact test (two-sided) with Bonferroni correction. For the heatmap, the Z score of the proportion of TE-containing coding and noncoding transcripts was computed. i Venn diagrams of the overlaps of the TE superfamilies with significant frequency differences in coding and noncoding transcripts. j TE frequencies of selected TEs in the coding and noncoding transcripts in the indicated cell states.