Global quantification of mammalian gene expression control

Abstract

SummaryGene expression is a multistep process that involves transcription, translation and turnover of mRNAs and proteins. Although it is one of the most fundamental processes of life, the entire cascade has never been quantified on a genome-wide scale. Here, we simultaneously measured mRNA and protein abundance and turnover by parallel metabolic pulse labeling for more than 5,000 genes in mammalian cells. While mRNA and protein levels correlated better than previously thought, corresponding half-lives showed no correlation. Employing a quantitative model we obtain the first genome-scale prediction of synthesis rates of mRNAs and proteins. We find that the cellular abundance of proteins is predominantly 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. Quantitative information about all stages of gene expression obtained in this study provides a rich resource and helps understanding the underlying design principles.

Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging

“…To obtain quantitative information about a broader range of centrosomal proteins, we subjected the above centrosome preparations to shotgun proteomics and estimated protein abundance using the iBAQ method (Schwanhausser et al , 2011; Arike et al , 2012; Ahrne et al , 2013). Figure 3 and Table EV2 summarize the results for 73 core centrosomal proteins [including 58/61 proteins described in Azimzadeh et al (2012)].…”

“…The database search results were filtered using the ion score to set the false discovery rate (FDR) to 1% on the peptide and protein level, respectively, based on the number of reverse protein sequence hits in the datasets. After normalizing the quantitative data of the technical replicates using the SafeQuant software tool (Glatter et al , 2012), the summed precursor intensities obtained from Progenesis for each centrosome preparation were aligned with the absolute protein concentrations determined by SRM analysis according to the iBAQ method (Schwanhausser et al , 2011), respectively. The resulting models were applied to estimate absolute protein levels for all proteins quantified in two centrosome preparations, and data were combined by calculating mean protein levels.…”

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2‐acidified sea water

“…The concentration of specific proteins is not only the result of transcription, but also the balance between mRNA degradation, translation, and protein degradation (Schwanhäusser, Busse, & Li, 2011). While stress can alter translation (Picard, Loubière, Girbal, & Cocaign‐Bousquet, 2013), mRNA degradation (Huch & Nissan, 2014), protein degradation (Flick & Kaiser, 2012), and protein activity (Krebs & Holbrook, 2001; Pan et al., 2015), transcriptomic regulation nonetheless can show a clear pattern of response to environmental stressors and, thus, indicate the involvement of genes and physiological processes in the organism's response (de Nadal et al., 2011; Evans & Hofmann, 2012; Evans & Watson‐Wynn, 2014; Anderson et al., 2015).…”

Integrative structure and functional anatomy of a nuclear pore complex

“…Raw MS files from QConCat Mlp1 immunoisolation experiments were analyzed by the MaxQuant iBAQ method 64 . Only non-isotopically labeled (not QConCat) peptides were considered.…”