Computational Regulatory Genomics

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The protein expression landscape of the Arabidopsis root

J. Petricka,  M. Schauer,  M. Megraw,  N. Breakfield,  J. Thompson,  S. Georgiev,  E. Soderblom,  Uwe Ohler,  M. Moseley,  U. Grossniklaus,  P. Benfey 
Proc. Natl. Acad. Sci. U.S.A. 2012 109 18 6811--6818 PubMed Central   DOI   PubMed  


Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.
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