Reference
Citation
Brown, J.B., Boley, N., Eisman, R., May, G.E., Stoiber, M.H., Duff, M.O., Booth, B.W., Wen, J., Park, S., Suzuki, A.M., Wan, K.H., Yu, C., Zhang, D., Carlson, J.W., Cherbas, L., Eads, B.D., Miller, D., Mockaitis, K., Roberts, J., Davis, C.A., Frise, E., Hammonds, A.S., Olson, S., Shenker, S., Sturgill, D., Samsonova, A.A., Weiszmann, R., Robinson, G., Hernandez, J., Andrews, J., Bickel, P.J., Carninci, P., Cherbas, P., Gingeras, T.R., Hoskins, R.A., Kaufman, T.C., Lai, E.C., Oliver, B., Perrimon, N., Graveley, B.R., Celniker, S.E. (2014). Diversity and dynamics of the Drosophila transcriptome.  Nature 512(7515): 393--399.
FlyBase ID
FBrf0225793
Publication Type
Research paper
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.
PubMed ID
PubMed Central ID
PMC4152413 (PMC) (EuropePMC)
Related Publication(s)
Supplementary material
Personal communication to FlyBase
modENCODE RNA-Seq data remapped to BDGP Release 6 genome assembly.
Brown et al., 2014.8.27, Nature: [FBrf0226107]
The D. melanogaster transcriptome: modENCODE RNA-Seq data for dissected tissues
Graveley et al., 2011.4.13, The D. melanogaster transcriptome: modENCODE RNA-Seq data for dissected tissues [FBrf0213503]
FlyBase analysis
Gene model annotation changes in release 6.02 precipitated by data in Brown et al, 2014.
FlyBase Genome Annotators, 2014, Gene model annotation changes in release 6.02 precipitated by data in Brown et al, 2014. [FBrf0225867]
Note
Genomics: Hiding in plain sight.
Muerdter and Stark, 2014, Nature 512(7515): 374--375 [FBrf0226644]
Discovering the complexity of the metazoan transcriptome.
Hangauer et al., 2014, Genome Biol. 15(4): 112 [FBrf0227924]
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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Nature
    Title
    Nature
    Publication Year
    1869-
    ISBN/ISSN
    0028-0836
    Data From Reference
    Genes (85)
    Datasets (323)
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    Cell Lines (23)