Combined use of RNAi and quantitative proteomics to study gene function in Drosophila.

Tiziana Bonaldi, Tobias Straub, Jürgen Cox, Chanchal Kumar, Peter B. Becker, Matthias Mann

Research output: Contribution to journalArticle

84 Citations (Scopus)

Abstract

RNA interference is a powerful way to study gene function and is frequently combined with microarray analysis. Here we introduce a similar technology at the protein level by simultaneously applying Stable Isotope Labeling by Amino acids in Cell culture (SILAC) and RNA interference (RNAi) to Drosophila SL2 cells. After knockdown of ISWI, an ATP-hydrolyzing motor of different chromatin remodeling complexes, we obtained a quantitative proteome of more than 4,000 proteins. ISWI itself was reduced 10-fold as quantified by SILAC. Several hundred proteins were significantly regulated and clustered into distinct functional categories. Acf-1, a direct interaction partner of ISWI, is severely depleted at the protein, but not the transcript, level; this most likely results from reduced protein stability. We found little overall correlation between changes in the transcriptome and proteome with many protein changes unaccompanied by message changes. However, correlation was high for those mRNAs that changed significantly by microarray.

Original languageEnglish
Pages (from-to)762-772
Number of pages11
JournalMolecular Cell
Volume31
Issue number5
Publication statusPublished - Sep 5 2008

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RNA Interference
Proteomics
Drosophila
Genes
Proteome
Proteins
Isotope Labeling
Chromatin Assembly and Disassembly
Protein Stability
Microarray Analysis
Transcriptome
Cell Culture Techniques
Adenosine Triphosphate
Technology
Amino Acids
Messenger RNA

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

Bonaldi, T., Straub, T., Cox, J., Kumar, C., Becker, P. B., & Mann, M. (2008). Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Molecular Cell, 31(5), 762-772.

Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. / Bonaldi, Tiziana; Straub, Tobias; Cox, Jürgen; Kumar, Chanchal; Becker, Peter B.; Mann, Matthias.

In: Molecular Cell, Vol. 31, No. 5, 05.09.2008, p. 762-772.

Research output: Contribution to journalArticle

Bonaldi, T, Straub, T, Cox, J, Kumar, C, Becker, PB & Mann, M 2008, 'Combined use of RNAi and quantitative proteomics to study gene function in Drosophila.', Molecular Cell, vol. 31, no. 5, pp. 762-772.
Bonaldi T, Straub T, Cox J, Kumar C, Becker PB, Mann M. Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Molecular Cell. 2008 Sep 5;31(5):762-772.
Bonaldi, Tiziana ; Straub, Tobias ; Cox, Jürgen ; Kumar, Chanchal ; Becker, Peter B. ; Mann, Matthias. / Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. In: Molecular Cell. 2008 ; Vol. 31, No. 5. pp. 762-772.
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