Alternative Polyadenylation Determines the Functional Landscape of Inverted Alu Repeats

Inverted Alu repeats (IRAlus) are abundantly found in the transcriptome, especially in introns and 3′ UTRs. Yet, the biological significance of IRAlus embedded in 3′ UTRs remains largely unknown. Here, we find that 3′ UTR IRAlus silence genes involved in essential signaling pathways. We utilize J2 antibody to directly capture and map the double-stranded RNA structure of 3′ UTR IRAlus in the transcriptome. Bioinformatic analysis reveals alternative polyadenylation as a major axis of IRAlus-mediated gene regulation. Notably, the expression of mouse double minute 2 (MDM2), an inhibitor of p53, is upregulated by the exclusion of IRAlus during UTR shortening, which is exploited to silence p53 during tumorigenesis. Moreover, the transcriptome-wide UTR lengthening in neural progenitor cells results in the global downregulation of genes associated with neurodegenerative diseases, including amyotrophic lateral sclerosis, via IRAlus inclusion. Our study establishes the functional landscape of 3′ UTR IRAlus and its role in human pathophysiology. mRNA-seq following subcellular fractionation in HeLa cells or A549 cells as well as J2 fCLIP-seq in NPCs or A549 cells. siLuc or a mixture of siCSTF2&siCSTF2T was transfected.