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The developmental transcriptome of Drosophila melanogaster.

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.

Pubmed ID: 21179090


  • Graveley BR
  • Brooks AN
  • Carlson JW
  • Duff MO
  • Landolin JM
  • Yang L
  • Artieri CG
  • van Baren MJ
  • Boley N
  • Booth BW
  • Brown JB
  • Cherbas L
  • Davis CA
  • Dobin A
  • Li R
  • Lin W
  • Malone JH
  • Mattiuzzo NR
  • Miller D
  • Sturgill D
  • Tuch BB
  • Zaleski C
  • Zhang D
  • Blanchette M
  • Dudoit S
  • Eads B
  • Green RE
  • Hammonds A
  • Jiang L
  • Kapranov P
  • Langton L
  • Perrimon N
  • Sandler JE
  • Wan KH
  • Willingham A
  • Zhang Y
  • Zou Y
  • Andrews J
  • Bickel PJ
  • Brenner SE
  • Brent MR
  • Cherbas P
  • Gingeras TR
  • Hoskins RA
  • Kaufman TC
  • Oliver B
  • Celniker SE



Publication Data

March 24, 2011

Associated Grants

  • Agency: NHLBI NIH HHS, Id: U01 HB004271
  • Agency: NHGRI NIH HHS, Id: U01 HG004271
  • Agency: NHGRI NIH HHS, Id: U01 HG004271-01
  • Agency: Intramural NIH HHS, Id: ZIA DK015600-14
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

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