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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


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.


  1. 1.

    Sex limited inheritance in Drosophila. Science 32, 120–122 (1910)

  2. 2.

    A gene complex controlling segmentation in Drosophila. Nature 276, 565–570 (1978)

  3. 3.

    & Mutations affecting segment number and polarity in Drosophila. Nature 287, 795–801 (1980)

  4. 4.

    et al. Comparative genomics of the eukaryotes. Science 287, 2204–2215 (2000)

  5. 5.

    Learning the common language of genetics. Genetics 174, 1–3 (2006)

  6. 6.

    et al. Gene expression during the life cycle of Drosophila melanogaster. Science 297, 2270–2275 (2002)

  7. 7.

    et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306, 655–660 (2004)

  8. 8.

    et al. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nature Genet. 38, 1151–1158 (2006)

  9. 9.

    RNA Editing (Oxford Univ. Press, 2001)

  10. 10.

    Illuminating the silence: understanding the structure and function of small RNAs. Nature Rev. Mol. Cell Biol. 8, 23–36 (2007)

  11. 11.

    , & Novel transcripts from the Ultrabithorax domain of the Bithorax Complex. Genes Dev. 1, 307–322 (1987)

  12. 12.

    , , , & roX1 RNA paints the X chromosome of male Drosophila and is regulated by the dosage compensation system. Cell 88, 445–457 (1997)

  13. 13.

    et al. Unlocking the secrets of the genome. Nature 459, 927–930 (2009)

  14. 14.

    et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science doi:10.1126/science.1198374. (in the press)

  15. 15.

    et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science doi:10.1126/science.1196914. (in the press)

  16. 16.

    et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441, 87–90 (2006)

  17. 17.

    , & A family of conserved noncoding elements derived from an ancient transposable element. Proc. Natl Acad. Sci. USA 103, 11659–11664 (2006)

  18. 18.

    et al. The abdominal region of the Bithorax Complex. Cell 43, 81–96 (1985)

  19. 19.

    , , & The molecular genetics of the bithorax complex of Drosophila cis-regulation in the Abdominal-B domain. EMBO J. 9, 4277–4286 (1990)

  20. 20.

    et al. Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. PLoS Genet. 5, e1000709 (2009)

  21. 21.

    & Spatially ordered transcription of regulatory DNA in the bithorax complex of Drosophila. Development 107, 321–329 (1989)

  22. 22.

    , , , & 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)

  23. 23.

    MicroRNAs in the Drosophila bithorax complex. Genes Dev. 22, 14–19 (2008)

  24. 24.

    et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 28, 511–515 (2010)

  25. 25.

    et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203–218 (2007)

  26. 26.

    & A revised model for U4atac/U6atac snRNA base pairing. RNA 8, 125–128 (2002)

  27. 27.

    , , & A conserved WD40 protein binds the Cajal body localization signal of scaRNP particles. Mol. Cell 34, 47–57 (2009)

  28. 28.

    et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. doi:10.1101/gr.112466.110. (in the press)

  29. 29.

    et al. A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. Genome Biol. 5, R40 (2004)

  30. 30.

    & Tissue-specific ecdysone responses: regulation of the Drosophila genes Eip28/29 and Eip40 during larval development. Development 116, 865–876 (1992)

  31. 31.

    , , & Molecular analysis of the initiation of insect metamorphosis: a comparative study of Drosophila ecdysteroid-regulated transcription. Dev. Biol. 160, 388–404 (1993)

  32. 32.

    & Temporal and spatial utilization of the alcohol dehydrogenase gene promoters during the development of Drosophila melanogaster. Dev. Biol. 134, 430–437 (1989)

  33. 33.

    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)

  34. 34.

    et al. A novel ecdysone receptor mediates steroid-regulated developmental events during the mid-third instar of Drosophila. PLoS Genet. 4, e1000102 (2008)

  35. 35.

    et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007)

  36. 36.

    , , & Most “dark matter” transcripts are associated with known genes. PLoS Biol. 8, e1000371 (2010)

  37. 37.

    , , , & Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genet. 40, 1413–1415 (2008)

  38. 38.

    et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008)

  39. 39.

    , & A computational and experimental approach toward a priori identification of alternatively spliced exons. RNA 10, 1838–1844 (2004)

  40. 40.

    Sex-determining mechanisms in insects. Int. J. Dev. Biol. 52, 837–856 (2008)

  41. 41.

    , & RNA editing in Drosophila melanogaster: New targets and functional consequences. RNA 12, 1922–1932 (2006)

  42. 42.

    & Genetic approaches to studying adenosine-to-inosine RNA editing. Methods Enzymol. 424, 265–287 (2007)

  43. 43.

    , , & Nervous system targets of RNA editing identified by comparative genomics. Science 301, 832–836 (2003)

  44. 44.

    & 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)

  45. 45.

    et al. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol. 5, R3 (2003)

  46. 46.

    et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219–232 (2007)

  47. 47.

    The transcriptional diversity of 25 Drosophila cell lines. Genome Res. doi:10.1101/gr.112961.110. (in the press)

  48. 48.

    Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415 (2003)

  49. 49.

    et al. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res. doi:10.1101/gr.108662.110. (in the press)

Download references


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.).

Author information

Author notes

    • Brenton R. Graveley
    • , Angela N. Brooks
    • , Joseph W. Carlson
    • , Michael O. Duff
    • , Jane M. Landolin
    •  & Li Yang

    These authors contributed equally to this work.


  1. Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-6403, USA

    • Brenton R. Graveley
    • , Michael O. Duff
    •  & Li Yang
  2. Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA

    • Angela N. Brooks
    •  & Steven E. Brenner
  3. Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

    • Joseph W. Carlson
    • , Jane M. Landolin
    • , Benjamin W. Booth
    • , Ann Hammonds
    • , Jeremy E. Sandler
    • , Kenneth H. Wan
    • , Roger A. Hoskins
    •  & Susan E. Celniker
  4. Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA

    • Carlo G. Artieri
    • , Renhua Li
    • , John H. Malone
    • , Nicolas R. Mattiuzzo
    • , David Sturgill
    • , Lichun Jiang
    • , Yu Zhang
    •  & Brian Oliver
  5. Center for Genome Sciences and Department of Computer Science, Washington University, St Louis, Missouri 63108, USA

    • Marijke J. van Baren
    • , Laura Langton
    •  & Michael R. Brent
  6. Department of Statistics, University of California, Berkeley, California, 94720 USA

    • Nathan Boley
    • , James B. Brown
    •  & Peter J. Bickel
  7. Center for Genomics and Bioinformatics, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA

    • Lucy Cherbas
    • , Dayu Zhang
    • , Yi Zou
    •  & Peter Cherbas
  8. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA

    • Carrie A. Davis
    • , Alex Dobin
    • , Wei Lin
    • , Chris Zaleski
    • , Phil Kapranov
    •  & Thomas R. Gingeras
  9. Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA

    • David Miller
    • , Brian Eads
    • , Justen Andrews
    • , Peter Cherbas
    •  & Thomas C. Kaufman
  10. Genetic Systems Division, Research and Development, Life Technologies, Foster City, California 94404, USA

    • Brian B. Tuch
  11. Genome Analysis Unit, Amgen, South San Francisco, California 94080, USA

    • Brian B. Tuch
  12. Stowers Institute for Medical Research, 1000 East 50th street, Kansas City, Missouri 64110, USA

    • Marco Blanchette
  13. Department of Pathology and Laboratory Medicine, Kansas University Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA

    • Marco Blanchette
  14. Division of Biostatistics, School of Public Health, University of California, Berkeley, California 94720, USA

    • Sandrine Dudoit
  15. Department of Biomolecular Engineering. University of California, Santa Cruz. Santa Cruz, California 95064, USA

    • Richard E. Green
  16. Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Norbert Perrimon
  17. Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA

    • Aarron Willingham
    •  & Steven E. Brenner
  18. Affymetrix, Santa Clara, California 95051, USA

    • Thomas R. Gingeras


  1. Search for Brenton R. Graveley in:

  2. Search for Angela N. Brooks in:

  3. Search for Joseph W. Carlson in:

  4. Search for Michael O. Duff in:

  5. Search for Jane M. Landolin in:

  6. Search for Li Yang in:

  7. Search for Carlo G. Artieri in:

  8. Search for Marijke J. van Baren in:

  9. Search for Nathan Boley in:

  10. Search for Benjamin W. Booth in:

  11. Search for James B. Brown in:

  12. Search for Lucy Cherbas in:

  13. Search for Carrie A. Davis in:

  14. Search for Alex Dobin in:

  15. Search for Renhua Li in:

  16. Search for Wei Lin in:

  17. Search for John H. Malone in:

  18. Search for Nicolas R. Mattiuzzo in:

  19. Search for David Miller in:

  20. Search for David Sturgill in:

  21. Search for Brian B. Tuch in:

  22. Search for Chris Zaleski in:

  23. Search for Dayu Zhang in:

  24. Search for Marco Blanchette in:

  25. Search for Sandrine Dudoit in:

  26. Search for Brian Eads in:

  27. Search for Richard E. Green in:

  28. Search for Ann Hammonds in:

  29. Search for Lichun Jiang in:

  30. Search for Phil Kapranov in:

  31. Search for Laura Langton in:

  32. Search for Norbert Perrimon in:

  33. Search for Jeremy E. Sandler in:

  34. Search for Kenneth H. Wan in:

  35. Search for Aarron Willingham in:

  36. Search for Yu Zhang in:

  37. Search for Yi Zou in:

  38. Search for Justen Andrews in:

  39. Search for Peter J. Bickel in:

  40. Search for Steven E. Brenner in:

  41. Search for Michael R. Brent in:

  42. Search for Peter Cherbas in:

  43. Search for Thomas R. Gingeras in:

  44. Search for Roger A. Hoskins in:

  45. Search for Thomas C. Kaufman in:

  46. Search for Brian Oliver in:

  47. Search for Susan E. Celniker in:


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.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Brenton R. Graveley or Susan E. Celniker.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    The file contains Supplementary Text, Supplementary references, Supplementary Figures 1-13 with legends and Supplementary Table legends 1-34.

  2. 2.

    Supplementary Table 35

    This file contains the Accession Numbers for RNA-seq, microarrays and cDNAs.  Supplementary Table 35 was added on 9 January 2011.

Zip files

  1. 1.

    Supplementary Tables

    The file contains Supplementary Tables 1-12.  The file extension name for Supplementary Table 10 was amended on January 9 2011.

  2. 2.

    Supplementary Tables

    The file contains Supplementary Tables 13-18.  The file extension name for Supplementary Table 18 was amended on January 9 2011.

  3. 3.

    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.

  4. 4.

    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.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.