Diversity of miRNAs, siRNAs and piRNAs surveyed across 25 Drosophila cell lines

The transcriptional diversity of a large panel of Drosophila cell lines was reported by the modENCODE consortium. We expanded this knowledge base by deeply sequencing their small RNAs. In total, our modENCODE project generated over 1 billion raw reads from 53 libraries across 25 cell lines, of which 38 datasets are new to this study. We analyze the reproducibility of sequence profiles of biological replicates, determine common and distinct aspects of miRNA expression across cell lines, and infer the global impact of miRNAs on cell line transcriptomes. We also characterize commonalities and differences in endo-siRNA populations across cell lines, including cis-NAT-siRNAs and TE-siRNAs. Interestingly, most cell lines exhibit enhanced TE-siRNA production relative to tissues, suggesting this as a common aspect of cell immortalization. We broadly extend the annotations of cell-restricted endo-siRNA loci, and also identify a set of common cis-NAT-siRNA loci with preferred activity across a broad set of cells and tissues. Finally, we characterize small RNAs in a set of ovary-derived cell lines, including somatic cells (OSS and OSC) and a mixed germline/somatic cell population (fGS/OSS) that exhibits ping-pong piRNA signatures. Together with the companion analysis of long RNAs, these small RNA data provide comprehensive information on the transcriptional landscape of diverse Drosophila cell lines. These data should encourage broader usage of Drosophila cell lines, beyond the few that are presently in common usage.

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