<i>Su(var)3</i>–<i>7</i> has a weak impact on transposon silencing, but regulates piRNA clusters transcription.

<p>(<b>A</b>) Quantitative RT-PCR analysis on 22 retrotransposons in <i>Su(var)3</i>–<i>7^R2a8</i> homozygous mutant ovaries (grey bars) and female carcasses (black bars). Histograms represent the fold changes in RNA levels relative to <i>Su(var)3</i>–<i>7^R2a8</i>/<i>TM6</i> siblings; error bars indicate the standard deviation of triplicate samples (n = 3). Differences in the fold changes were tested by a Welch t-test (* : p<0,05; ** : p<0,01). (<b>B</b>) Quantitative RT-PCR analysis of <i>cluster 2</i> and <i>flamenco</i> from control (<i>w¹¹¹⁸</i>) and <i>Su(var)3</i>–<i>7^R2a8</i> heterozygote and homozygote mutant ovaries. Shown are the fold changes in RNA levels relative to the control (n = 3; * : p<0,05). The position of the primer sets used for qRT-PCR are indicated by bars named 1, 2 and 3 along the map above. Coordinates of the clusters along the <i>X</i> chromosome are indicated in Mb. Boxes indicate protein coding genes (blue) and transposon fragments in sense (black) and antisense (red) orientation. (<b>C</b>) Quantitative RT-PCR analysis of <i>cluster1</i> from control (<i>w¹¹¹⁸</i>) and <i>Su(var)3</i>–<i>7^R2a8</i> heterozygote and homozygote mutants. Shown are the fold changes in RNA levels relative to the control (n = 3; * : p<0,05). A map of the <i>cluster1</i>/<i>42AB</i> locus with position of the qPCR primer sets 4 and 5 is shown above. (<b>D</b>) Histograms show the log2 fold ratios of normalized ovarian piRNAs mapping antisense to transposons (left) and uniquely mapping piRNAs (sense plus antisense) over piRNA clusters (right) between homozygous and heterozygous <i>Su(var)3</i>–<i>7</i> mutants. Up to 1 mismatch was allowed between reads and transposon sequences.