Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes

Through an integrative analysis of genome-wide predictions of highly stable RNA duplexes, alternative splicing profiles, and proximity ligation-detection of RNA-RNA interactions in vivo, we observe evidence that the majority of long-range intronic RNA duplexes are mediated by inverted Alu-repeat elements, and that these structures are associated with widespread exon skipping in primates.

Our results further reveal evidence that Alu-derived RNA duplexes have contributed to divergence in alternative splicing patterns during mammalian evolution.