Fig. 4

CCC depletion differentially affects esiRNA biogenesis from retroTns and inverted repeat loci. a Ratios of percent miRNAs, transpsoson (Tn)-derived and hairpin (hp)-derived siRNAs from Symplekin (pink), CPSF73 (red), and Dcr2 (blue) knockdown samples are shown. Percentages are the total miRNA, Tn or hp normalized read count (reads per million mapped (RPMM)) divided by the total normalized read count (summed normalized miRNA, pre-miRNA, Tn, non-coding RNA, and hp RPMs). The percents of each smRNA group were normalized to the LacZ control. Error bars represent one standard deviation. b CPSF73 and Symplekin RNAi-depleted samples are represented as in a. RPMMs of esiRNAs mapping to hp loci Esi1 and Esi2 in Symp and CPSF73 depleted samples were normalized to corresponding esiRNAs in LacZ samples (left). RPMMs of RNA-seq reads mapping to sense (S) precursors of Esi1 and Esi2 RNA in these knockdowns were also normalized to corresponding RNA-seq reads in LacZ samples (right). Error bars are as in a. c RPMMs of esiRNAs mapping to Dm297, mdg1 and jockey retroTns in Symp and CPSF73 depleted samples were normalized to corresponding esiRNAs in LacZ samples (left). RPMMs of RNA-seq reads mapping to sense (S) and antisense (AS) precursors of Dm297, mdg1, jockey transcripts in these knockdowns were also normalized to corresponding RNA-seq reads in LacZ samples (right). Error bars are as in a