Intronic Alus Influence Alternative Splicing

TL;DR

This study reveals that intronic Alu elements significantly influence alternative splicing in humans by forming dsRNA structures that alter exon inclusion, highlighting their role in transcriptome evolution.

Contribution

It provides experimental evidence that intronic Alus can base-pair and modulate splicing modes, a novel insight into Alu's functional impact on gene regulation.

Findings

Alus are more common near alternatively spliced exons.

Alu insertions can switch exons from constitutive to alternative splicing.

Inverted Alus form dsRNA affecting downstream exon splicing.

Abstract

Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. A large fraction of Alus are found in intronic sequences, implying extensive Alu-Alu dsRNA formation in mRNA precursors. Yet, the effect of these intronic Alus on splicing of the flanking exons is largely unknown. Here, we show that more Alus flank alternatively spliced exons than constitutively spliced ones; this is especially notable for those exons that have changed their mode of splicing from constitutive to alternative during human evolution. This implies that Alu insertions may change the mode of splicing of the flanking exons. Indeed, we demonstrate experimentally that two Alu elements that were inserted into an intron in opposite orientation undergo base-pairing, as evident by RNA editing, and affect the splicing patterns of a downstream exon, shifting it from constitutive to alternative. Our results indicate the importance of intronic Alus in influencing the splicing of flanking exons, further emphasizing the role of Alus in shaping of the human transcriptome