The Developmental Transcriptome of Drosophila Melanogaster

Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22.

Abstract

Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alternative Splicing / genetics
  • Animals
  • Base Sequence
  • Drosophila Proteins / genetics
  • Drosophila melanogaster / embryology
  • Drosophila melanogaster / genetics*
  • Drosophila melanogaster / growth & development*
  • Exons / genetics
  • Female
  • Gene Expression Profiling*
  • Gene Expression Regulation, Developmental / genetics*
  • Genes, Insect / genetics
  • Genome, Insect / genetics
  • Male
  • MicroRNAs / genetics
  • Oligonucleotide Array Sequence Analysis
  • Protein Isoforms / genetics
  • RNA Editing / genetics
  • RNA, Messenger / analysis
  • RNA, Messenger / genetics
  • RNA, Small Untranslated / analysis
  • RNA, Small Untranslated / genetics
  • Sequence Analysis
  • Sex Characteristics
  • Transcription, Genetic / genetics*

Substances

  • Drosophila Proteins
  • MicroRNAs
  • Protein Isoforms
  • RNA, Messenger
  • RNA, Small Untranslated