De novo TE insertions near genes impart PIWI-mediated gene silencing. (A) Heat map of top PIWI-regulated genes identified in OSS cells with low CLIP scores and which have a de novo TE insertion nearby. (B) Nascent transcript profiles for two loci that contain de novo TE insertions and are strongly regulated by PIWI silencing. Arrows point to the changing levels of reads for genes and the independent nascent transcripts arising from the TE insertion. (C) Genomic PCR confirms these persistent TE insertions specifically in the OSS_C line. “E” and “C” represent early and current passage of cells (see Fig. 3A). These are persistent TE insertions because no reference genome amplicon (the lowest band) is detected. Asterisks mark side-product amplicons. (D) Venn diagram showing distinct group of PIWI-regulated genes between OSCs and OSS cells. (E) Genomic PCR shows TE insertions specific to the OSC cells. (Left panel) Genes noted in Sienski et al. (2012); (right panel) additional insertions near genes we validated in OSC cell genomes. These are heterogeneous TE insertions because a reference genome amplicon is detected in addition to the TE amplicon. Asterisks mark side-product amplicons.
