Fig. 2.

Splicing of transposable elements into genes. RNA-Seq data from mouse ESCs showing the control (shLuc) or a knockdown of the RING finger domain, polycomb 1 protein RNF2 (shRnf2), that leads to the activation of expression of two genes: Nat8f2 (panel A) and Apol7b (panel B). For each genomic view, the first row shows the short-read RNA-Seq read pileup density in the control (shLuc; red) and knockdown (shRnf2; blue) experiments. The second row shows the novel splice junctions detected in the RNA-Seq data when Rnf2 is knocked down (shRnf2). Splice junctions that join an exon of Nat8f2 or Apol7b to an LTR are indicated in red, other splice junctions are indicated in grey. The third row shows the GENCODE genes at this locus. The fourth row shows the locations of the LTRs (red), SINEs (green) and LINEs (blue). LTRs that show evidence of splicing into Nat8f2 or Apol7b are labeled. Data is from GSE108091 [147]. Reads were aligned to the mm10 genome using STAR [111], with the parameters described in [147]. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)