Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

Recent large-scale quantitative assessment of the proteome and transcriptome has revealed that transcript abundances only partially predict protein abundances. This article discusses ways in which such studies are informing our knowledge of protein expression regulation. Recent advances in next-generation DNA sequencing and proteomics provide an unprecedented ability to survey mRNA and protein abundances. Such proteome-wide surveys are illuminating the extent to which different aspects of gene expression help to regulate cellular protein abundances. Current data demonstrate a substantial role for regulatory processes occurring after mRNA is made — that is, post-transcriptional, translational and protein degradation regulation — in controlling steady-state protein abundances. Intriguing observations are also emerging in relation to cells following perturbation, single-cell studies and the apparent evolutionary conservation of protein and mRNA abundances. Here, we summarize current understanding of the major factors regulating protein expression.