Cleavage site heterogeneity at the pre-mRNA 3'-untranslated region regulates gene expression

Abstract

Endonucleolytic cleavage step of the eukaryotic mRNA 3'-end processing is considered imprecise that leads to heterogeneity of cleavage site (CS) with hitherto unknown function. Contrary to the popular belief, we show that this imprecision in cleavage is tightly regulated resulting in CS heterogeneity (CSH) that controls gene expression in antioxidant response. CSH centres at a primary CS followed by a number of subsidiary cleavages that is determined by the position of the CS. Globally and by using reporter antioxidant NQO1 mRNA, we discovered an inverse relationship between the number of CS and the gene expression with the primary CS exhibiting highest cleavage efficiency. Strikingly, reducing CSH and increasing primary CS usage induces gene expression. Under oxidative stress condition (tBHQ, H2O2 or NaAsO2), there is a decrease in the CSH and an increase in the primary CS usage to induce antioxidant gene expression. Concomitantly, ectopic NQO1 expression from the primary CS or reduction in CSH imparts cellular oxidative stress tolerance. Genome-wide CS analysis of stress response genes also shows a concomitant result. We show that oxidative stress induces affinity/strength of cleavage complex assembly increasing the fidelity of cleavage at the primary CS thereby reducing CSH inducing antioxidant response.