Abstract
The relationships between the levels of transcripts and the levels of the proteins they encode have not been examined comprehensively in mammals, although previous work in plants and yeast suggest a surprisingly modest correlation. We have examined this issue using a genetic approach in which natural variations were used to perturb both transcript levels and protein levels among inbred strains of mice. We quantified over 5,000 peptides and over 22,000 transcripts in livers of 97 inbred and recombinant inbred strains and focused on the 7,185 most heritable transcripts and 486 most reliable proteins. The transcript levels were quantified by microarray analysis in three replicates and the proteins were quantified by Liquid Chromatography–Mass Spectrometry using O(18)-reference-based isotope labeling approach. We show that the levels of transcripts and proteins correlate significantly for only about half of the genes tested, with an average correlation of 0.27, and the correlations of transcripts and proteins varied depending on the cellular location and biological function of the gene. We examined technical and biological factors that could contribute to the modest correlation. For example, differential splicing clearly affects the analyses for certain genes; but, based on deep sequencing, this does not substantially contribute to the overall estimate of the correlation. We also employed genome-wide association analyses to map loci controlling both transcript and protein levels. Surprisingly, little overlap was observed between the protein- and transcript-mapped loci. We have typed numerous clinically relevant traits among the strains, including adiposity, lipoprotein levels, and tissue parameters. Using correlation analysis, we found that a low number of clinical trait relationships are preserved between the protein and mRNA gene products and that the majority of such relationships are specific to either the protein levels or transcript levels. Surprisingly, transcript levels were more strongly correlated with clinical traits than protein levels. In light of the widespread use of high-throughput technologies in both clinical and basic research, the results presented have practical as well as basic implications.
Highlights
An underlying assumption in many biological studies is the concordance of transcript and protein levels during the flow of information from DNA to phenotype
An old dogma in biology states that, in every cell, the flow of biological information is from DNA to RNA to proteins and that the latter act as a working force to determine the organism’s phenotype
We show that the relationship between various biological traits is not simple and that there is relatively little concordance of RNA levels and the corresponding protein levels in response to DNA perturbations
Summary
Ethics statement All animals were handled in strict accordance with good animal practice as defined by the relevant national and/or local animal welfare bodies, and all animal work was approved by the appropriate committee. At 16 weeks of age, whole body fat, fluids and lean tissue mass of mice were determined using a Bruker Optics Minispec nuclear magnetic resonance (NMR) analyzer (The Woodlands, TX, USA) according to the manufacturer’s recommendations. We calculated the total mass of the mice, sum of lean mass, free fluid, and fat mass, and body fat percentage, fat mass/total mass. Glucose levels were determined using commercially available kits from Sigma (St Louis, MO, USA). Insulin levels were measured using commercial ELISA kits (ALPCO Diagnostics). Mice were euthanized by cervical dislocation and the mass of individual tissues and fat depots (heart, kidney, retroperitoneal fat pad, epididymal fat pad, subcutaneous fat pad, and omental fat pad) were determined by dissecting and weighing each tissue/pad separately after the mice were euthanized. Liver tissues were dissected out, flash frozen in liquid nitrogen, and kept at 270 degrees until further processing
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