Fig. 5: BmVasa preferentially binds to transposon mRNAs in vivo.
a, b Pie charts show the proportions of transposon mRNAs (blue) and protein-coding mRNAs (green) in the total RNA sequencing library (Total; left) and in the BmVasa FAST-iCLIP library (BmVasa binding; right), both of which were individually produced in BmN4 cells (Control) (a) and in BmN4 cells lacking Siwi-piRISC (Siwi-piRISC KD) (b). The association between the data is statistically significant (X 2 = 56,205, df = 1, p value <2.2 × 10−16, by Pearson’s chi-squared test (Two-tailed)) (a), (X 2 = 60,140, df = 1, p value <2.2 × 10−16, by Pearson’s chi-squared test (Two-tailed)) (b). c Scatter plots show correlation between RPKM values of the total RNA sequencing library (Total) and RPM values of the BmVasa FAST-iCLIP library (BmVasa binding) for protein-coding mRNAs (green; top) or transposon mRNAs (blue; bottom). ρ is Spearman’s rank correlation coefficient. d Scatter plots (left) show RPKM values of the total RNA sequencing library (Total; top) or RPM values of the BmVasa FAST-iCLIP library (BmVasa binding; bottom) for transposon mRNAs. They were categorized by the FCs in the expression levels of the mRNAs produced in BmN4 cells lacking Siwi-piRISC (Siwi-piRISC KD) relative to controls into “High” (red, log2 FC > 2, n = 8), “Middle” (green, 1 < log2 FC ≦2, n = 58), or “Low” (blue, log2 FC ≦1, n = 323). Box plots (right) show the FCs as in the scatter plots. Two-tailed Mann–Whitney U test was performed and p values are indicated on the box plots. Center line: median. Box limits: upper and lower quartiles. Whiskers: 1.5× interquartile range. e Bar graphs show the length distribution (8,000 nt or less) of protein-coding mRNAs (upper 3 graphs) and transposon mRNAs (lower 3 graphs). RPKM values of the BmVasa FAST-iCLIP library (BmVasa binding; top), RPKM values of the total RNA sequencing library (Total; middle), and the enrichment value (BmVasa binding relative to Total; bottom) are respectively indicated. Source data are provided as a Source Data file.
