title: Diversity and dynamics of the Drosophila transcriptome.
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.
authors.forename: James B
authors.initials: JB
authors.lastname: Brown
authors.forename: Nathan
authors.initials: N
authors.lastname: Boley
authors.forename: Robert
authors.initials: R
authors.lastname: Eisman
authors.forename: Gemma E
authors.initials: GE
authors.lastname: May
authors.forename: Marcus H
authors.initials: MH
authors.lastname: Stoiber
authors.forename: Michael O
authors.initials: MO
authors.lastname: Duff
authors.forename: Ben W
authors.initials: BW
authors.lastname: Booth
authors.forename: Jiayu
authors.initials: J
authors.lastname: Wen
authors.forename: Soo
authors.initials: S
authors.lastname: Park
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Suzuki
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wan
authors.forename: Charles
authors.initials: C
authors.lastname: Yu
authors.forename: Dayu
authors.initials: D
authors.lastname: Zhang
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Carlson
authors.forename: Lucy
authors.initials: L
authors.lastname: Cherbas
authors.forename: Brian D
authors.initials: BD
authors.lastname: Eads
authors.forename: David
authors.initials: D
authors.lastname: Miller
authors.forename: Keithanne
authors.initials: K
authors.lastname: Mockaitis
authors.forename: Johnny
authors.initials: J
authors.lastname: Roberts
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.forename: Erwin
authors.initials: E
authors.lastname: Frise
authors.forename: Ann S
authors.initials: AS
authors.lastname: Hammonds
authors.forename: Sara
authors.initials: S
authors.lastname: Olson
authors.forename: Sol
authors.initials: S
authors.lastname: Shenker
authors.forename: David
authors.initials: D
authors.lastname: Sturgill
authors.forename: Anastasia A
authors.initials: AA
authors.lastname: Samsonova
authors.forename: Richard
authors.initials: R
authors.lastname: Weiszmann
authors.forename: Garret
authors.initials: G
authors.lastname: Robinson
authors.forename: Juan
authors.initials: J
authors.lastname: Hernandez
authors.forename: Justen
authors.initials: J
authors.lastname: Andrews
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bickel
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
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: Eric C
authors.initials: EC
authors.lastname: Lai
authors.forename: Brian
authors.initials: B
authors.lastname: Oliver
authors.forename: Norbert
authors.initials: N
authors.lastname: Perrimon
authors.forename: Brenton R
authors.initials: BR
authors.lastname: Graveley
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D004331:Drosophila melanogaster / Q000033:anatomy & histology / Q000166:cytology / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D008297:Male; D058977:Molecular Sequence Annotation; D009417:Nerve Tissue / Q000378:metabolism; D009928:Organ Specificity; D011061:Poly A / Q000235:genetics; D026723:Polyadenylation; D011401:Promoter Regions, Genetic / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012727:Sex Characteristics; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D011061:Poly A