title: Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation.
abstract: BACKGROUND
  Genome-wide transcriptome analyses have given systems-level insights into gene regulatory networks. Due to the limited depth of quantitative proteomics, however, our understanding of post-transcriptional gene regulation and its effects on protein-complex stoichiometry are lagging behind.
  
  
  RESULTS
  Here, we employ deep sequencing and the isobaric tag for relative and absolute quantification (iTRAQ) technology to determine transcript and protein expression changes of a Drosophila brain tumor model at near genome-wide resolution. In total, we quantify more than 6,200 tissue-specific proteins, corresponding to about 70% of all transcribed protein-coding genes. Using our integrated data set, we demonstrate that post-transcriptional gene regulation varies considerably with biological function and is surprisingly high for genes regulating transcription. We combine our quantitative data with protein-protein interaction data and show that post-transcriptional mechanisms significantly enhance co-regulation of protein-complex subunits beyond transcriptional co-regulation. Interestingly, our results suggest that only about 11% of the annotated Drosophila protein complexes are co-regulated in the brain. Finally, we refine the composition of some of these core protein complexes by analyzing the co-regulation of potential subunits.
  
  
  CONCLUSIONS
  Our comprehensive transcriptome and proteome data provide a valuable resource for quantitative biology and offer novel insights into understanding post-transcriptional gene regulation in a tumor model.
authors.forename: Christoph
authors.initials: C
authors.lastname: Jüschke
authors.forename: Ilse
authors.initials: I
authors.lastname: Dohnal
authors.forename: Peter
authors.initials: P
authors.lastname: Pichler
authors.forename: Heike
authors.initials: H
authors.lastname: Harzer
authors.forename: Remco
authors.initials: R
authors.lastname: Swart
authors.forename: Gustav
authors.initials: G
authors.lastname: Ammerer
authors.forename: Karl
authors.initials: K
authors.lastname: Mechtler
authors.forename: Juergen A
authors.initials: JA
authors.lastname: Knoblich
mesh_terms: D000818:Animals; D001932:Brain Neoplasms / Q000235:genetics*; D019295:Computational Biology; D004249:DNA Damage; D004260:DNA Repair; D004261:DNA Replication; D015536:Down-Regulation; D004330:Drosophila / Q000235:genetics*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D049750:Genome, Insect; D059014:High-Throughput Nucleotide Sequencing; D011499:Protein Processing, Post-Translational / Q000235:genetics*; D020543:Proteome / Q000235:genetics*; D040901:Proteomics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D020543:Proteome; D012333:RNA, Messenger