Diversity and dynamics of the Drosophila transcriptome

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 () and Susan E. Celniker ()
Additional contact information
James B. Brown: University of California Berkeley
Nathan Boley: University of California Berkeley
Robert Eisman: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Gemma E. May: Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA
Marcus H. Stoiber: University of California Berkeley
Michael O. Duff: Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA
Ben W. Booth: Lawrence Berkeley National Laboratory
Jiayu Wen: Sloan-Kettering Institute, 1017C Rockefeller Research Labs, 1275 York Avenue, Box 252, New York, New York 10065, USA
Soo Park: Lawrence Berkeley National Laboratory
Ana Maria Suzuki: RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
Kenneth H. Wan: Lawrence Berkeley National Laboratory
Charles Yu: Lawrence Berkeley National Laboratory
Dayu Zhang: Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Joseph W. Carlson: Lawrence Berkeley National Laboratory
Lucy Cherbas: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Brian D. Eads: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
David Miller: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Keithanne Mockaitis: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Johnny Roberts: Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Carrie A. Davis: Cold Spring Harbor Laboratory
Erwin Frise: Lawrence Berkeley National Laboratory
Ann S. Hammonds: Lawrence Berkeley National Laboratory
Sara Olson: Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA
Sol Shenker: Sloan-Kettering Institute, 1017C Rockefeller Research Labs, 1275 York Avenue, Box 252, New York, New York 10065, USA
David Sturgill: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Anastasia A. Samsonova: Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
Richard Weiszmann: Lawrence Berkeley National Laboratory
Garret Robinson: University of California Berkeley
Juan Hernandez: University of California Berkeley
Justen Andrews: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Peter J. Bickel: University of California Berkeley
Piero Carninci: RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
Peter Cherbas: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Thomas R. Gingeras: Cold Spring Harbor Laboratory
Roger A. Hoskins: Lawrence Berkeley National Laboratory
Thomas C. Kaufman: Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405, USA
Eric C. Lai: Sloan-Kettering Institute, 1017C Rockefeller Research Labs, 1275 York Avenue, Box 252, New York, New York 10065, USA
Brian Oliver: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Norbert Perrimon: Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
Brenton R. Graveley: Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA
Susan E. Celniker: Lawrence Berkeley National Laboratory

Nature, 2014, vol. 512, issue 7515, 393-399

Abstract: 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.

Date: 2014
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DOI: 10.1038/nature12962

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