Diversity and dynamics of the Drosophila transcriptome

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. (March 2014) Diversity and dynamics of the Drosophila transcriptome. Nature, 512 (7515). pp. 393-399. ISSN 0028-0836

URL: http://www.ncbi.nlm.nih.gov/pubmed/24670639
DOI: 10.1038/nature12962

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.

Item Type: Paper
Subjects: organism description > animal > insect > Drosophila
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: Matt Covey
Date: 16 March 2014
Date Deposited: 11 Apr 2014 20:07
Last Modified: 06 Apr 2015 18:49
PMCID: PMC4152413
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29731

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving