Genetic Basis of Alternative Polyadenylation as an Emerging Molecular Phenotype for Human Traits and Diseases

Genome-wide association studies have identified thousands of non-coding variants that are statistically associated with human traits and diseases. However, functional interpretation of these variants remains a major challenge. Here, we describe the first atlas of human 3'-UTR alternative polyadenylation (APA) Quantitative Trait Loci (3'aQTLs), i.e. ~0.4 million genetic variants associated with APA of target genes across 46 Genotype-Tissue Expression (GTEx) tissues from 467 individuals. APA occurs in approximately 70% of human genes and substantively impacts cellular proliferation, differentiation and tumorigenesis. Mechanistically, 3'aQTLs could alter polyA motifs and RNA-binding protein binding sites, leading to thousands of APA changes. Importantly, 3'aQTLs can be used to interpret ~16.1% of trait-associated variants and are largely distinct from other QTLs such as eQTLs. These 3'aQTLs thus represent the genetic basis of APA as a novel molecular phenotype to explain a large fraction of non-coding variants and to provide new insights into complex traits and disease etiologies. Overall design: Examination of alternative polyadenylation and gene expression upon LARP4 KD in HEK293T cells.