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.
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Accession codes
Data deposits
All sequence data have been deposited in the SRA, cDNA sequences have been deposited in GenBank, and array data deposited in GEO (see Supplementary Table 35 for all accession numbers). All data is also available at http://www.modencode.org.
References
Morgan, T. H. Sex limited inheritance in Drosophila . Science 32, 120–122 (1910)
Lewis, E. B. A gene complex controlling segmentation in Drosophila . Nature 276, 565–570 (1978)
Nüsslein-Volhard, C. & Wieschaus, E. Mutations affecting segment number and polarity in Drosophila . Nature 287, 795–801 (1980)
Rubin, G. M. et al. Comparative genomics of the eukaryotes. Science 287, 2204–2215 (2000)
Spradling, A. C. Learning the common language of genetics. Genetics 174, 1–3 (2006)
Arbeitman, M. N. et al. Gene expression during the life cycle of Drosophila melanogaster . Science 297, 2270–2275 (2002)
Stolc, V. et al. A gene expression map for the euchromatic genome of Drosophila melanogaster . Science 306, 655–660 (2004)
Manak, J. R. et al. Biological function of unannotated transcription during the early development of Drosophila melanogaster . Nature Genet. 38, 1151–1158 (2006)
Bass, B. L. RNA Editing (Oxford Univ. Press, 2001)
Rana, T. M. Illuminating the silence: understanding the structure and function of small RNAs. Nature Rev. Mol. Cell Biol. 8, 23–36 (2007)
Lipshitz, H. D., Peattie, D. A. & Hogness, D. S. Novel transcripts from the Ultrabithorax domain of the Bithorax Complex. Genes Dev. 1, 307–322 (1987)
Meller, V. H., Wu, K. H., Roman, G., Kuroda, M. I. & Davis, R. L. roX1 RNA paints the X chromosome of male Drosophila and is regulated by the dosage compensation system. Cell 88, 445–457 (1997)
Celniker, S. E. et al. Unlocking the secrets of the genome. Nature 459, 927–930 (2009)
The modENCODE Consortium et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science doi:10.1126/science.1198374. (in the press)
Gerstein, M. B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science doi:10.1126/science.1196914. (in the press)
Bejerano, G. et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441, 87–90 (2006)
Xie, X., Kamal, M. & Lander, E. S. A family of conserved noncoding elements derived from an ancient transposable element. Proc. Natl Acad. Sci. USA 103, 11659–11664 (2006)
Karch, F. et al. The abdominal region of the Bithorax Complex. Cell 43, 81–96 (1985)
Celniker, S. E., Sharma, S., Keelan, D. & Lewis, E. B. The molecular genetics of the bithorax complex of Drosophila cis-regulation in the Abdominal-B domain. EMBO J. 9, 4277–4286 (1990)
Ho, M. C. et al. Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila . PLoS Genet. 5, e1000709 (2009)
Sanchez-Herrero, E. & Akam, M. Spatially ordered transcription of regulatory DNA in the bithorax complex of Drosophila . Development 107, 321–329 (1989)
Bae, E., Calhoun, V. C., Levine, M., Lewis, E. B. & Drewell, R. A. Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc. Natl Acad. Sci. USA 99, 16847–16852 (2002)
Bender, W. MicroRNAs in the Drosophila bithorax complex. Genes Dev. 22, 14–19 (2008)
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 28, 511–515 (2010)
Clark, A. G. et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203–218 (2007)
Padgett, R. A. & Shukla, G. C. A revised model for U4atac/U6atac snRNA base pairing. RNA 8, 125–128 (2002)
Tycowski, K. T., Shu, M. D., Kukoyi, A. & Steitz, J. A. A conserved WD40 protein binds the Cajal body localization signal of scaRNP particles. Mol. Cell 34, 47–57 (2009)
Hoskins, R. A. et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. doi:10.1101/gr.112466.110. (in the press)
Parisi, M. et al. A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. Genome Biol. 5, R40 (2004)
Andres, A. J. & Cherbas, P. Tissue-specific ecdysone responses: regulation of the Drosophila genes Eip28/29 and Eip40 during larval development. Development 116, 865–876 (1992)
Andres, A. J., Fletcher, J. C., Karim, F. D. & Thummel, C. S. Molecular analysis of the initiation of insect metamorphosis: a comparative study of Drosophila ecdysteroid-regulated transcription. Dev. Biol. 160, 388–404 (1993)
Lockett, T. J. & Ashburner, M. Temporal and spatial utilization of the alcohol dehydrogenase gene promoters during the development of Drosophila melanogaster . Dev. Biol. 134, 430–437 (1989)
Warren, J. T. et al. Discrete pulses of molting hormone, 20-hydroxyecdysone, during late larval development of Drosophila melanogaster: correlations with changes in gene activity. Dev. Dyn. 235, 315–326 (2006)
Costantino, B. F. et al. A novel ecdysone receptor mediates steroid-regulated developmental events during the mid-third instar of Drosophila . PLoS Genet. 4, e1000102 (2008)
Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007)
van Bakel, H., Nislow, C., Blencowe, B. J. & Hughes, T. R. Most “dark matter” transcripts are associated with known genes. PLoS Biol. 8, e1000371 (2010)
Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genet. 40, 1413–1415 (2008)
Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008)
Philipps, D. L., Park, J. W. & Graveley, B. R. A computational and experimental approach toward a priori identification of alternatively spliced exons. RNA 10, 1838–1844 (2004)
Sanchez, L. Sex-determining mechanisms in insects. Int. J. Dev. Biol. 52, 837–856 (2008)
Stapleton, M., Carlson, J. W. & Celniker, S. E. RNA editing in Drosophila melanogaster: New targets and functional consequences. RNA 12, 1922–1932 (2006)
Jepson, J. E. & Reenan, R. A. Genetic approaches to studying adenosine-to-inosine RNA editing. Methods Enzymol. 424, 265–287 (2007)
Hoopengardner, B., Bhalla, T., Staber, C. & Reenan, R. Nervous system targets of RNA editing identified by comparative genomics. Science 301, 832–836 (2003)
Wang, J. W. & Wu, C. F. Modulation of the frequency response of Shaker potassium channels by the quiver peptide suggesting a novel extracellular interaction mechanism. J. Neurogenet. 24, 67–74 (2010)
Hild, M. et al. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol. 5, R3 (2003)
Stark, A. et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219–232 (2007)
Cherbas, L. The transcriptional diversity of 25 Drosophila cell lines. Genome Res. doi:10.1101/gr.112961.110. (in the press)
Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415 (2003)
Brooks, A. N. et al. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res. doi:10.1101/gr.108662.110. (in the press)
Acknowledgements
We thank C. Trapnell and L. Pachter for discussions and assistance with Cufflinks, and E. Clough for comments and feedback. A.N.B. was partially supported by an NSF graduate fellowship. This work was funded by an award from the National Human Genome Research INstitute modENCODE Project (U01 HB004271) to S.E.C. (Principal Investigator) and M.R.B., P.C., T.R.G., B.R.G. and N.P. (co-Principal Investigators) under Department of Energy contract no. DE-AC02-05CH11231, and by the National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program (B.O.).
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J.A., M.R.B., P.C., T.R.G., B.R.G., R.A.H., T.C.K., B.O., N.P. and S.E.C. designed the project. J.A., S.E.B., M.R.B., P.C., T.R.G., B.R.G., R.A.H., B.O. and S.E.C. managed the project. D.M. prepared biological samples. T.C.K. oversaw biological sample production. D.Z. and B.E. prepared RNA samples. J.A. oversaw RNA sample production. W.L. and A.W. analysed array data. P.K. managed array data production. L.Y. prepared Illumina RNA-Seq libraries. C.A.D., L.L., J.E.S., K.H.W. and L.Y. performed Illumina sequencing. J.M.L., B.R.G. and S.E.C. managed Illumina sequencing production. M.B. and R.E.G. performed 454 sequencing of adults. R.A.H. managed production of the embryonic SOLiD and 454 sequencing. C.A.D. managed data transfers. C.Z. managed databases and formatted array and sequence data for submission. C.G.A., P.J.B., S.E.B., A.N.B., S.D., M.O.D., B.R.G. and D.S. developed analysis methods. C.G.A., J.B.B., N.B., B.W.B., S.E.B., A.N.B., J.W.C., S.E.C., L.C., P.C., C.A.D., A.D., M.O.D., B.R.G., R.L., J.H.M., N.R.M., D.S. and Yi.Z. analysed data. B.B.T. aligned the SOLiD data. M.J.V. and J.M.L. generated annotations. C.G.A., D.S. and J.H.M. analysed species validation data. L.J., C.G.A., D.S. and N.R.M. performed species RNA-Seq quality control. Yu.Z. and J.H.M. oversaw sequencing and gathered species samples. C.G.A., A.N.B., J.W.C., L.C., P.C., A.H., D.S., J.M.L., R.L. N.R.M., J.H.M. and B.O. contributed to the text. A.H. assisted with manuscript preparation. B.R.G. and S.E.C. wrote the paper with input from all authors. All authors discussed the results and commented on the manuscript.
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Supplementary information
Supplementary Information
The file contains Supplementary Text, Supplementary references, Supplementary Figures 1-13 with legends and Supplementary Table legends 1-34. (PDF 3767 kb)
Supplementary Tables
The file contains Supplementary Tables 1-12. The file extension name for Supplementary Table 10 was amended on January 9 2011. (ZIP 11757 kb)
Supplementary Tables
The file contains Supplementary Tables 13-18. The file extension name for Supplementary Table 18 was amended on January 9 2011. (ZIP 22949 kb)
Supplementary Tables
The file contains Supplementary Tables 19-26. The file extension names for Supplementary Tables 19 and 22 were amended on January 9 2011. (ZIP 18901 kb)
Supplementary Tables
The file contains Supplementary Tables 27-34. The file extension names for Supplementary Tables 27 and 28 were amended on January 9 2011. (ZIP 17989 kb)
Supplementary Table 35
This file contains the Accession Numbers for RNA-seq, microarrays and cDNAs. Supplementary Table 35 was added on 9 January 2011. (PDF 222 kb)
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Graveley, B., Brooks, A., Carlson, J. et al. The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (2011). https://doi.org/10.1038/nature09715
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DOI: https://doi.org/10.1038/nature09715
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