title: The developmental transcriptome of Drosophila melanogaster.
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.
authors.affiliation: Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-6403, USA. graveley@neuron.uchc.edu
authors.forename: Brenton R
authors.initials: BR
authors.lastname: Graveley
authors.forename: Angela N
authors.initials: AN
authors.lastname: Brooks
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Carlson
authors.forename: Michael O
authors.initials: MO
authors.lastname: Duff
authors.forename: Jane M
authors.initials: JM
authors.lastname: Landolin
authors.forename: Li
authors.initials: L
authors.lastname: Yang
authors.forename: Carlo G
authors.initials: CG
authors.lastname: Artieri
authors.forename: Marijke J
authors.initials: MJ
authors.lastname: van Baren
authors.forename: Nathan
authors.initials: N
authors.lastname: Boley
authors.forename: Benjamin W
authors.initials: BW
authors.lastname: Booth
authors.forename: James B
authors.initials: JB
authors.lastname: Brown
authors.forename: Lucy
authors.initials: L
authors.lastname: Cherbas
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.forename: Alex
authors.initials: A
authors.lastname: Dobin
authors.forename: Renhua
authors.initials: R
authors.lastname: Li
authors.forename: Wei
authors.initials: W
authors.lastname: Lin
authors.forename: John H
authors.initials: JH
authors.lastname: Malone
authors.forename: Nicolas R
authors.initials: NR
authors.lastname: Mattiuzzo
authors.forename: David
authors.initials: D
authors.lastname: Miller
authors.forename: David
authors.initials: D
authors.lastname: Sturgill
authors.forename: Brian B
authors.initials: BB
authors.lastname: Tuch
authors.forename: Chris
authors.initials: C
authors.lastname: Zaleski
authors.forename: Dayu
authors.initials: D
authors.lastname: Zhang
authors.forename: Marco
authors.initials: M
authors.lastname: Blanchette
authors.forename: Sandrine
authors.initials: S
authors.lastname: Dudoit
authors.forename: Brian
authors.initials: B
authors.lastname: Eads
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
authors.forename: Ann
authors.initials: A
authors.lastname: Hammonds
authors.forename: Lichun
authors.initials: L
authors.lastname: Jiang
authors.forename: Phil
authors.initials: P
authors.lastname: Kapranov
authors.forename: Laura
authors.initials: L
authors.lastname: Langton
authors.forename: Norbert
authors.initials: N
authors.lastname: Perrimon
authors.forename: Jeremy E
authors.initials: JE
authors.lastname: Sandler
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wan
authors.forename: Aarron
authors.initials: A
authors.lastname: Willingham
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Yi
authors.initials: Y
authors.lastname: Zou
authors.forename: Justen
authors.initials: J
authors.lastname: Andrews
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bickel
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
authors.forename: Michael R
authors.initials: MR
authors.lastname: Brent
authors.forename: Peter
authors.initials: P
authors.lastname: Cherbas
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
authors.forename: Roger A
authors.initials: RA
authors.lastname: Hoskins
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Kaufman
authors.forename: Brian
authors.initials: B
authors.lastname: Oliver
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics* / Q000254:growth & development*; D005091:Exons / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D017344:Genes, Insect / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics; D008297:Male; D035683:MicroRNAs / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D020033:Protein Isoforms / Q000235:genetics; D017393:RNA Editing / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D058727:RNA, Small Untranslated / Q000032:analysis / Q000235:genetics; D017421:Sequence Analysis; D012727:Sex Characteristics; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D029721:Drosophila Proteins; D035683:MicroRNAs; D020033:Protein Isoforms; D012333:RNA, Messenger; D058727:RNA, Small Untranslated