Fig. 5

CCC factor RNAi-depletion may alter hairpin secondary structure a Potential secondary structures for Tns (left) and hps (right). Complementary regions are shown in green and magenta. b Depletion of CCC components does not cause 3’ end misprocessing of retroTn transcripts. S and AS RNA-seq reads from LacZ (control), Symplekin, and CPSF73 RNAi-depleted samples were visualized using the UCSC genome browser and are overlayed. Schematic of a genomic region containing a mdg1 element is shown above the bedgraph. No unique reads are observed flanking the retroTn. c CG6903 read-through transcripts could hybridize to Esi2 RNAs in CCC factor knockdowns. Symplekin (blue), CPSF73 (green) depleted samples and LacZ (red) control RNA mapping to this region are shown. RNA-seq data is displayed in the top two panels, siRNA-seq data is displayed in the bottom panel