Integrated genomic and proteomic analyses of gene expression in Mammalian cells

TitleIntegrated genomic and proteomic analyses of gene expression in Mammalian cells
Publication TypeJournal Article
Year of Publication2004
AuthorsTian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE
JournalMol Cell Proteomics
Date PublishedOct
Keywords*Gene Expression Regulation, *Genomics, *Proteomics, Animals, Cell Line, Culture Media, Conditioned, Electrophoresis, Gel, Two-Dimensional, Genetic Variation, Hematopoietic Stem Cells/cytology, Kinetics, Liver/drug effects, Male, Mass Spectrometry, Mice, Mice, Inbred C57BL, Myeloid Progenitor Cells/cytology, Myelopoiesis, Oligonucleotide Array Sequence Analysis, Peroxisome Proliferator-Activated Receptors/agonists, Peroxisome Proliferators/pharmacology, Protein Processing, Post-Translational, Proteins/analysis/metabolism, Pyrimidines/pharmacology, RNA, Messenger/analysis/metabolism, Thiazolidinediones/pharmacology
AbstractUsing DNA microarrays together with quantitative proteomic techniques (ICAT reagents, two-dimensional DIGE, and MS), we evaluated the correlation of mRNA and protein levels in two hematopoietic cell lines representing distinct stages of myeloid differentiation, as well as in the livers of mice treated for different periods of time with three different peroxisome proliferative activated receptor agonists. We observe that the differential expression of mRNA (up or down) can capture at most 40% of the variation of protein expression. Although the overall pattern of protein expression is similar to that of mRNA expression, the incongruent expression between mRNAs and proteins emphasize the importance of posttranscriptional regulatory mechanisms in cellular development or perturbation that can be unveiled only through integrated analyses of both proteins and mRNAs.