Year: 2014
Type: article
Abstract: Animal transcriptomes are dynamic, with each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. Here we have identified new genes, transcripts and proteins using poly(A)+ RNA sequencing from Drosophila melanogaster in cultured cell lines, dissected organ systems and under environmental perturbations. We found that a small set of mostly neural-specific genes has the potential to encode thousands of transcripts each through extensive alternative promoter usage and RNA splicing. The magnitudes of splicing changes are larger between tissues than between developmental stages, and most sex-specific splicing is gonad-specific. Gonads express hundreds of previously unknown coding and long non-coding RNAs (lncRNAs), some of which are antisense to protein-coding genes and produce short regulatory RNAs. Furthermore, previously identified pervasive intergenic transcription occurs primarily within newly identified introns. The fly transcriptome is substantially more complex than previously recognized, with this complexity arising from combinatorial usage of promoters, splice sites and polyadenylation sites. A large-scale transcriptome analysis in Drosophila melanogaster, across tissues, cell types and conditions, provides insights into global patterns and diversity of transcription initiation, splicing, polyadenylation and non-coding RNA expression.
Source: Nature
DOI: 10.1038/nature12962
Authors: James B. Brown, Nathan Boley, Robert Eisman, Gemma E. May, Marcus H. Stoiber, Michael O. Duff, Ben W. Booth, Jiayu Wen, Soo Park, Ana Maria Suzuki, Kenneth H. Wan, Charles Yu, Dayu Zhang, Joseph W. Carlson, Lucy Cherbas, Brian D. Eads, David Miller, Keithanne Mockaitis, Johnny Roberts, Carrie A. Davis, Erwin Frise, Ann S. Hammonds, Sara Olson, Sol Shenker, David Sturgill, Anastasia A. Samsonova, Richard Weiszmann, Garret Robinson, Juan Hernandez, Justen Andrews, Peter J. Bickel, Piero Carninci, Peter Cherbas, Thomas R. Gingeras, Roger A. Hoskins, Thomas C. Kaufman, Eric C. Lai, Brian Oliver, Norbert Perrimon, Brenton R. Graveley, Susan E. Celniker
Institutions: Lawrence Berkeley National Laboratory, University of California, Berkeley, Indiana University Bloomington, Indiana University, UConn Health, RIKEN, Cold Spring Harbor Laboratory, National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Howard Hughes Medical Institute, Harvard University
Language: English
Topic: RNA Research and Splicing
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $12,690
Awards: G1286236842, G1308078171, G134308097, G216544311, G2258455552, G2617648412, Patterned Gene Expression in Drosophila Development, G3083819904, G3346463861, G346540353, G3796758151, G3936247624, G3969225054, G3993517178, G42916606, Annotation of the small RNA/microRNA component Drosophila genome, Comprehensive characterization of the Drosophila transcriptome, G5259372774, A Data Analysis Center for integration of fly and worm modENCODE datasets, G666505512, G6697452419, G6713907200, G8448016098, G9000030908, Cancer Center Support Grant, Selective regulatory and biogenesis mechanisms for microRNAs, CSHL Cancer Center Support Grant, G969889393
OpenAlex ID: W2097401587