title: Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines.
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.
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
authors.forename: Jiayu
authors.initials: J
authors.lastname: Wen
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA; Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA;
authors.forename: Jaaved
authors.initials: J
authors.lastname: Mohammed
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
authors.forename: Diane
authors.initials: D
authors.lastname: Bortolamiol-Becet
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
authors.forename: Harrison
authors.initials: H
authors.lastname: Tsai
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA; New York Genome Center, New York, New York 10022, USA;
authors.forename: Nicolas
authors.initials: N
authors.lastname: Robine
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
authors.forename: Jakub O
authors.initials: JO
authors.lastname: Westholm
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
authors.forename: Erik
authors.initials: E
authors.lastname: Ladewig
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
authors.forename: Qi
authors.initials: Q
authors.lastname: Dai
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA; Temasek Life Sciences, Temasek Lifesciences Laboratory, National University of Singapore, 117604 Singapore;
authors.forename: Katsutomo
authors.initials: K
authors.lastname: Okamura
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
authors.forename: Alex S
authors.initials: AS
authors.lastname: Flynt
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Dayu
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Justen
authors.initials: J
authors.lastname: Andrews
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Lucy
authors.initials: L
authors.lastname: Cherbas
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Kaufman
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Cherbas
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA;
authors.forename: Adam
authors.initials: A
authors.lastname: Siepel
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA;
authors.forename: Eric C
authors.initials: EC
authors.lastname: Lai
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D019295:Computational Biology / Q000379:methods; D004330:Drosophila / Q000235:genetics*; D015870:Gene Expression; D056426:Genetic Loci; D014644:Genetic Variation; D005854:Germ Cells; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering