Diversity and dynamics of the Drosophila transcriptome

Research output: Contribution to journalArticle

Authors

  • 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

Colleges, School and Institutes

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.

Details

Original languageEnglish
Pages (from-to)393-9
Number of pages7
JournalNature
Volume512
Issue number7515
Publication statusPublished - 28 Aug 2014

Keywords

  • Alternative Splicing, Animals, Drosophila melanogaster, Female, Gene Expression Profiling, Male, Molecular Sequence Annotation, Nerve Tissue, Organ Specificity, Poly A, Polyadenylation, Promoter Regions, Genetic, RNA, Long Noncoding, RNA, Messenger, Sex Characteristics, Stress, Physiological, Transcriptome, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.