Figure 4. Analysis of endo-siRNA and piRNA origin with respect to a collection of transposon master control loci in the Drosophila genome.

Fifteen transposon containing genomic regions were reported as master regulators of transposon activity [23]. The reads from each library were separated in endo-siRNAs (21 nt) and piRNAs (24-27 nt) by their length, then mapped allowing only those reads that matched uniquely among these clusters to be retained. The counts were normalized to cluster length as well as to total genome matching reads (reads per kilobase per million mapped reads, RPKM). Cluster 2 (chromosome X; 20A), 8 (chromosome X; 20 A-B, also known as flamenco), 13 (chromosome 3LHet) and 15 (chromosome 3LHet) are shown. In the soma cluster 2 showed an excessive amount of a unique sequence at a particular location in the homozygous mutant r2d2 sample after β-elimination. This likely represents a technical artifact and was therefore omitted. We specifically label the results after exclusion of the special sequence with **.