Transcriptome-wide analyses of piRNA binding sites. (A) To investigate in vivo small RNA binding regulation, we analyzed in vivo binding site data, in silico predicted piRNA targeting site data, and small RNA targeting site data. Synthesizing these data sets allowed us to identify small RNA binding patterns across groups of genes and within genomic features. By comparing such patterns in distinct genetic mutants, we infer and propose possible regulatory mechanisms of piRNA silencing. (B) Two examples highlight distinct patterns observed between in vivo piRNA binding sites and in silico predicted piRNA targeting sites. The locations of predicted piRNA targeting sites are shown in red, the experimentally identified piRNA binding sites are shown in blue, and the common sites (defined as sites where the same piRNA was determined by prediction and experimentally to target overlapping mRNA regions) are shown in yellow. The specific regions of the indicated mRNAs, including 5′ UTR, CDS, and 3′ UTR, are also labeled.
