Regulatory dynamics of untranslated RNA (UTR) at the mRNA 3’-end - implications in gene expression

Abstract

Untranslated RNA (UTR) at the 3’-end of a messenger RNA (mRNA) plays an essential role in gene expression. It is marked by addition of a long poly(A)-tail that occurs in two concerted steps - endonucleolytic cleavage followed by polyadenylation. Poly(A) polymerase (PAP) carries out polyadenylation in a cleavage and polyadenylation (CPA) complex associated with >85 protein components. Canonical PAPα/γ is the primary PAP for mRNA polyadenylation in the nucleus. We have identified a variant non-canonical PAP, Star-PAP that selects mRNAs for polyadenylation. Unlike PAPα, Star-PAP targets do not require certain canonical cis-elements such as the U-rich downstream sequence and instead harbor an -AUA- motif sandwiched in a GC rich region for Star-PAP binding. In addition, they are dispensable of canonical CPA factors CstF-64 or WDR33 that recognize the polyadenylation site, and instead require additional coregulator protein RBM10 to assemble the CPA complex. This specificity of target mRNA selection is in turn modulated by kinases including casein kinase, protein kinase C, or phosphatidyl inositol kinase, PIPKI affecting Star-PAP-RBM10 nexus to regulates key cellular processes and disease pathology.

Interestingly, over 70% of human genes have multiple PA-sites at the 3′-UTR that are alternately used (alternative polyadenylation, APA) generating more than one mRNA isoform with different UTR lengths. Changes in the UTR length alter protein expression, and/or affect protein function. We have shown that Star-PAP regulates APA genome wide of genes particularly involved in cardiovascular diseases such as hypertrophy and heart failure. Inherent downregulation of Star-PAP or RBM10 during cardiac hypertrophy results in the PA-site shift altering overall hypertrophy gene program. In addition to the polyadenylation step, cleavage step is also critical in gene control during cardiac remodeling in hypertrophy. We have shown a regulated cleavage imprecision resulting cleavage site (CS) heterogeneity (CSH) centring around a primary CS versus several subsidiary CS affecting gene expression. We discovered an inverse relationship between CSH and antioxidant gene expression on hypertrophic induction. A decrease in the CSH and an increase in the primary CS usage induces antioxidant gene expression. Hypertrophic stimulus stimulates oxidative stress, yet the antioxidant response progressively goes down with hypertrophic progression. This is mediated by compromised CSH from Star-PAP down regulation underscoring the critical role of the two steps of 3’-end processing in the gene regulation.