Transcriptome and proteome quantification of a tumor model provides novel insights into post‐transcriptional gene regulationReport as inadecuate

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Genome Biology

, 14:r133

First Online: 30 November 2013Received: 12 July 2013Accepted: 30 November 2013


BackgroundGenome‐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.

ResultsHere, 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.

ConclusionsOur 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.

List of abbreviationsACNacetonitrile

AGCautomatic gain control

bpbase pair

CDScoding sequence

CIDcollisional‐induced dissociation

DPiMDrosophila protein interaction map

eIF3eukaryotic initiation factor 3

ETDelectron transfer dissociation

FAformic acid

FDRfalse discovery rate

FPKMfragments per kilobase of transcript per million mapped fragments

HCDhigher energy C‐trap dissociation

iTRAQisobaric tag for relative and absolute quantification

KEGGKyoto Encyclopedia of Genes and Genomes

LC‐MS-MSliquid chromatography‐tandem mass spectrometry

MCMminichromosome maintenance complex


PCRpolymerase chain reaction

rRNAribosomal RNA

SCXstrong cation exchange

SRMselected reaction monitoring

TEABtriethylammonium bicarbonate

TRiC-CCTTCP‐1 ring complex or chaperonin‐containing TCP‐1 complex

UTRuntranslated region.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2013-14-11-r133 contains supplementary material, which is available to authorized users.

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Author: Christoph Jüschke - Ilse Dohnal - Peter Pichler - Heike Harzer - Remco Swart - Gustav Ammerer - Karl Mechtler - Juergen A


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