Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., Brown, J.B., Cherbas, L., Davis, C.A., Dobin, A., Li, R., Lin, W., Malone, J.H., Mattiuzzo, N.R., Miller, D., Sturgill, D., Tuch, B.B., Zaleski, C., Zhang, D., Blanchette, M., Dudoit, S., Eads, B., Green, R.E., Hammonds, A., Jiang, L., Kapranov, P., Langton, L., Perrimon, N., Sandler, J.E., Wan, K.H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P.J., Brenner, S.E., Brent, M.R., Cherbas, P., Gingeras, T.R., Hoskins, R.A., Kaufman, T.C., Oliver, B., Celniker, S.E. (2011). The developmental transcriptome of Drosophila melanogaster.  Nature 471(7339): 473--479.

FBrf0213330

Research paper

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.

PMC3075879 (PMC) (EuropePMC)