Cell Reports
Volume 5, Issue 5, 12 December 2013, Pages 1469-1478
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Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

https://doi.org/10.1016/j.celrep.2013.10.041Get rights and content
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Highlights

  • Integrative genomics study of two inbred rat strains with different genetic backgrounds

  • Largest proteomics data resource for liver tissue to date: 13,088 proteins identified

  • Genes, splice variants, and RNA edits uncovered at the peptide level

  • A human GWAS top hit for hypertension, Cyp17a1 is strongly deregulated in SHR rats

Summary

Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and posttranscriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We obtained peptide evidence for 26,463 rat liver proteins. We validated 1,195 gene predictions, 83 splice events, 126 proteins with nonsynonymous variants, and 20 isoforms with nonsynonymous RNA editing. Quantitative RNA sequencing and proteomics data correlate highly between strains but poorly among each other, indicating extensive nongenetic regulation. Our multilevel analysis identified a genomic variant in the promoter of the most differentially expressed gene Cyp17a1, a previously reported top hit in genome-wide association studies for human hypertension, as a potential contributor to the hypertension phenotype in SHR rats. These results demonstrate the power of and need for integrative analysis for understanding genetic control of molecular dynamics and phenotypic diversity in a system-wide manner.

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These authors contributed equally to this work

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Present address: Departments of Chemistry and Biochemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ Oxford, UK

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Present address: European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan, 1, Building 3226, 9713 AV Groningen, the Netherlands