A genome-wide parallel quantification of mRNA and protein levels and turnover in mammalian cells was performed using parallel metabolic pulse labeling. The study measured mRNA and protein abundance and turnover for more than 5,000 genes in mammalian cells. mRNA and protein levels showed a better correlation than previously thought, while their half-lives did not correlate. A quantitative model was used to predict the synthesis rates of mRNAs and proteins on a genome-wide scale. The study found that protein abundance is primarily controlled at the level of translation. Genes with similar combinations of mRNA and protein stabilities shared functional properties, suggesting that half-lives evolved under energetic and dynamic constraints. The quantitative information obtained provides a rich resource for understanding the underlying design principles of gene expression. The study used pulse labeling with radioactive nucleosides or amino acids, and non-radioactive tracers, to measure mRNA and protein half-lives. The results showed that proteins were on average five times more stable than mRNAs and spanned a larger dynamic range. There was no correlation between protein and mRNA half-lives. Absolute cellular mRNA and protein copy numbers were calculated based on sequencing data and mass spectrometry. The study found that mRNA levels explained around 40% of the variability in protein levels, which is higher than in previous studies. The data also showed that translation rate constants played the dominant role in controlling protein levels. The study also found that genes with similar combinations of mRNA and protein half-lives shared functional properties, suggesting that half-lives evolved under energetic and dynamic constraints. The study further found that genes with unstable mRNAs and proteins were enriched in transcription factors, signaling genes, and chromatin modifying enzymes. Genes with stable mRNAs and unstable proteins were enriched in terms related to processing of mRNAs, tRNAs, and non-coding RNAs. The study also found that genes with stable mRNAs and unstable proteins were enriched in extracellular proteins, which is expected since secreted proteins have a short cellular half-life. The study concluded that gene expression is a complex process that involves multiple steps, and that the data provides a comprehensive understanding of the dynamics of gene expression in mammalian cells. The study also highlighted the importance of translational control for gene expression and the role of energy constraints in the evolution of gene expression. The data provides a valuable resource for the scientific community and can be used to further refine the understanding of gene expression in mammalian cells.A genome-wide parallel quantification of mRNA and protein levels and turnover in mammalian cells was performed using parallel metabolic pulse labeling. The study measured mRNA and protein abundance and turnover for more than 5,000 genes in mammalian cells. mRNA and protein levels showed a better correlation than previously thought, while their half-lives did not correlate. A quantitative model was used to predict the synthesis rates of mRNAs and proteins on a genome-wide scale. The study found that protein abundance is primarily controlled at the level of translation. Genes with similar combinations of mRNA and protein stabilities shared functional properties, suggesting that half-lives evolved under energetic and dynamic constraints. The quantitative information obtained provides a rich resource for understanding the underlying design principles of gene expression. The study used pulse labeling with radioactive nucleosides or amino acids, and non-radioactive tracers, to measure mRNA and protein half-lives. The results showed that proteins were on average five times more stable than mRNAs and spanned a larger dynamic range. There was no correlation between protein and mRNA half-lives. Absolute cellular mRNA and protein copy numbers were calculated based on sequencing data and mass spectrometry. The study found that mRNA levels explained around 40% of the variability in protein levels, which is higher than in previous studies. The data also showed that translation rate constants played the dominant role in controlling protein levels. The study also found that genes with similar combinations of mRNA and protein half-lives shared functional properties, suggesting that half-lives evolved under energetic and dynamic constraints. The study further found that genes with unstable mRNAs and proteins were enriched in transcription factors, signaling genes, and chromatin modifying enzymes. Genes with stable mRNAs and unstable proteins were enriched in terms related to processing of mRNAs, tRNAs, and non-coding RNAs. The study also found that genes with stable mRNAs and unstable proteins were enriched in extracellular proteins, which is expected since secreted proteins have a short cellular half-life. The study concluded that gene expression is a complex process that involves multiple steps, and that the data provides a comprehensive understanding of the dynamics of gene expression in mammalian cells. The study also highlighted the importance of translational control for gene expression and the role of energy constraints in the evolution of gene expression. The data provides a valuable resource for the scientific community and can be used to further refine the understanding of gene expression in mammalian cells.