Ku limits aberrant mRNA splicing promoted by intronic antisense Alu elements

Abstract

Alu elements are short repeats that occupy approximately 10% of the human genome 1,2. Saturation of primate genomes with Alu sequences occurred at the prosimian/new-world monkey evolutionary juncture. Alu elements have clearly driven unique aspects of higher primate evolution, but their presence can be detrimental to genomic stability 3. The expansion of Alu sequences in the genomes of higher primates precisely coincides with a substantial increase in the ubiquitous expression of the three polypeptides of the DNA-dependent protein kinase (DNA-PK), the Ku70/80 heterodimer and DNA-PKcs 4. Previous work suggests that the elevated levels of Ku70/80 are required to prevent the activation of innate immune signaling pathways triggered by RNA molecules derived from Alu elements 5. Here we demonstrate that Ku ablation dramatically alters mRNA splicing, by allowing the use of alternative splice sites contained in intronic antisense Alu elements, which are known to directly associate with Ku70/80 5. Dysregulation of mRNA splicing precedes cell death and preferentially impacts genes involved in essential RNA metabolism processes, including splicing and ribosome biogenesis, likely impacting cell viability. In addition, we demonstrate that cell death after Ku70 depletion cannot be rescued by expression of its prosimian homologue, which suggests that primate Ku70 has evolved specific molecular features to suppress deleterious effects of an Alu element rich genome. We propose a model in which Ku binding of antisense Alu elements in introns of nascent RNAs modulates the use of alternative splice sites to balance beneficial and detrimental contributions of Alu repeats within primate genomes.