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

Endonucleolytic cleavage step of the pre-mRNA 3'-end processing is imprecise and results in heterogeneity of cleavage site (CS). On the contrary, we show that cleavage imprecision is tightly regulated leading to CS heterogeneity (CSH) and controls antioxidant response gene expression. CSH centres at a primary CS followed by subsidiary cleavages determined by the position of the CS. Globally and using targeted antioxidant mRNAs, we discovered an inverse relationship between the number of CS and the gene expression with highest cleavage efficiency from the primary CS. Strikingly, reducing CSH and increasing primary CS usage induces gene expression. Under oxidative stress (tBHQ, H2O2 or NaAsO2), CSH is decreased and the primary CS usage is stimulated that induces antioxidant response gene expression. Concomitantly, ectopic anti-oxidant protein 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.