Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines (original) (raw)

1. Jaaved Mohammed1,2,3,
2. Diane Bortolamiol-Becet1,
3. Harrison Tsai1,
4. Nicolas Robine1,4,
5. Jakub O. Westholm1,
6. Erik Ladewig1,
7. Qi Dai1,
8. Katsutomo Okamura1,5,
9. Alex S. Flynt1,
10. Dayu Zhang6,
11. Justen Andrews6,
12. Lucy Cherbas6,
13. Thomas C. Kaufman6,
14. Peter Cherbas6,
15. Adam Siepel2 and
16. Eric C. Lai1,7
17. 1Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
18. 2Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA;
19. 3Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA;
20. 4New York Genome Center, New York, New York 10022, USA;
21. 5Temasek Life Sciences, Temasek Lifesciences Laboratory, National University of Singapore, 117604 Singapore;
22. 6Department of Biology, Indiana University, Bloomington, Indiana 47405, USA

Abstract

We expanded the knowledge base for Drosophila cell line transcriptomes by deeply sequencing their small RNAs. In total, we analyzed more than 1 billion raw reads from 53 libraries across 25 cell lines. We verify reproducibility of biological replicate data sets, determine common and distinct aspects of miRNA expression across cell lines, and infer the global impact of miRNAs on cell line transcriptomes. We next characterize their commonalities and differences in endo-siRNA populations. Interestingly, most cell lines exhibit enhanced TE-siRNA production relative to tissues, suggesting this as a common aspect of cell immortalization. We also broadly extend annotations of _cis_-NAT-siRNA loci, identifying ones with common expression across diverse cells and tissues, as well as cell-restricted loci. 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. Collectively, the ovary data reveal new genic piRNA loci, including unusual configurations of piRNA-generating regions. Together with the companion analysis of mRNAs described in a previous study, these small RNA data provide comprehensive information on the transcriptional landscape of diverse Drosophila cell lines. These data should encourage broader usage of fly cell lines, beyond the few that are presently in common usage.

Footnotes

• ↵7 Corresponding author
  E-mail laie{at}mskcc.org

• [Supplemental material is available for this article.]

• Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.161554.113.
  Freely available online through the Genome Research Open Access option.

• Received June 5, 2013.

• Accepted November 13, 2013.

• © 2014 Wen et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.