RT Journal Article SR Electronic T1 Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea JF bioRxiv FD Cold Spring Harbor Laboratory SP 033613 DO 10.1101/033613 A1 Sinan U. Umu A1 Anthony M. Poole A1 Renwick C.J. Dobson A1 Paul P. Gardner YR 2016 UL http://biorxiv.org/content/early/2016/03/23/033613.abstract AB A critical assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We also demonstrate a strong selection for avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.