Global identification of functional microRNA-mRNA interactions in Drosophila

MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. To close this gap, we generated the first transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-Seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila. Overall design: 1) Endogenous AGO1 PARCLIP and HITSCLIP small RNA sequencing data of wt Drosophila S2 cells. 2) smallRNA-seq data of endogenously 5'phosphorylated small RNA species wt Drosophila S2 cells. 3) Stranded, single-end, rRNA-depleted RNA-seq data upon dsRNA-mediated knockdown of AGO1 and control treatments. 4) Matched ribosomal footprinting data upon dsRNA-mediated knockdown of AGO1 and control treatments.