Multiple competing RNA structures dynamically control alternative splicing in human ATE1 gene

Abstract

The mammalian Ate1 gene encodes an arginyl transferase enzyme, which is essential for embryogenesis, male meiosis, and regulation of the cytoskeleton. Reduced levels of Ate1 are associated with malignant transformations and serve as a prognostic indicator of prostate cancer metastasis. The tumor suppressor function of Ate1 depends on the inclusion of one of the two mutually exclusive exons (MXE), exons 7a and 7b. Here, we report that the molecular mechanism underlying MXE splicing in Ate1 involves five conserved regulatory intronic elements R1-R5, of which R1 and R4 compete for base pairing with R3, while R2 and R5 form an ultra-long-range RNA structure spanning 30 Kb. In minigenes, single and double mutations that disrupt base pairings in R1R3 and R3R4 lead to the loss of MXE splicing, while compensatory triple mutations that restore the RNA structure also revert splicing to that of the wild type. Blocking the competing base pairings by locked nucleic acid (LNA)/DNA mixmers complementary to R3 leads to the loss of MXE splicing, while the disruption of the ultra-long-range R2R5 interaction changes the ratio of mutually exclusive isoforms in the endogenous Ate1 pre-mRNA. The upstream exon 7a becomes more included than the downstream exon 7b in response to RNA Pol II slowdown, however it fails to do so when the ultra-long-range R2R5 interaction is disrupted. In sum, we demonstrated that mutually exclusive splicing in Ate1 is controlled by two independent, dynamically interacting and functionally distinct RNA structure modules. The molecular mechanism proposed here opens new horizons for the development of therapeutic solutions, including antisense correction of splicing.