Systematic identification of functional SNPs interrupting 3’UTR polyadenylation signals

Abstract

Alternative polyadenylation (APA) is emerging as a widespread regulatory layer since the majority of human protein-coding genes contain several polyadenylation (p(A)) sites in their 3'UTRs. By generating isoforms with different 3'UTR length, APA potentially affects mRNA stability, translation efficiency, nuclear export, and cellular localization. Polyadenylation sites are regulated by adjacent RNA cis-regulatory elements, the principals among them are the polyadenylation signal (PAS) AAUAAA and its main variant AUUAAA, typically located 20-nt upstream of the p(A) site. Mutations in PAS and other auxiliary poly(A) cis-elements in the 3'UTR of several genes have been shown to cause human Mendelian diseases, and to date, only a few common SNPs that regulate APA were associated with complex diseases. Here, we systematically searched for SNPs that affect gene expression and human traits by modulation of 3'UTR APA. First, focusing on the variants most likely to exert the strongest effect, we identified 2,305 SNPs that interrupt the canonical PAS or its main variant. Implementing pA-QTL tests using GTEx RNA-seq data, we identified 330 PAS SNPs (called PAS pA-QTLs) that were significantly associated with the usage of their p(A) site. As expected, PAS-interrupting alleles were mostly linked with decreased cleavage at their p(A) site and the consequential 3'UTR lengthening. However, interestingly, in~10% of the cases, the PAS-interrupting allele was associated with increased usage of an upstream p(A) site and 3'UTR shortening. As an indication of the functional effects of these PAS pA-QTLs on gene expression and complex human traits, we observed for few dozens of them marked colocalization with eQTL and/or GWAS signals. The PAS-interrupting alleles linked with 3'UTR lengthening were also strongly associated with decreased gene expression, indicating that shorter isoforms generated by APA are generally more stable than longer ones. Last, we carried out an extended, genome-wide analysis of 3'UTR variants and detected thousands of additional pA-QTLs having weaker effects compared to the PAS pA-QTLs.

MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome

“…These cis-acting motifs all have in common with the MREs interacting with miRISC that they affect the stability of mRNAs in certain tissues and/or developmental stages [88][89][90]. There were also 18 over-represented motifs that had the PAS-motif (AATAAA) [11,91]. The PAS-motif function is to initiate poly-adenylation from a certain position in the 3 UTR of the precursor mRNA.…”

“…MicroSalmon may be used as a starting point to retrieve cis-acting motifs (both MREs and others) in FL-transcripts of interest, which can be validated by experimental methods. Furthermore, it may serve as a reference for targeted HTS studies to identify genetic variation that affect the function of such elements [91,101,107,108]. MicroSalmon also represents a resource for the discovery of transcript variants that are differently regulated due to alternative polyadenylation of the 3 UTRs.…”

CRISPRpas: programmable regulation of alternative polyadenylation by dCas9

“…Mutations changing the PAS strength have been reported in a growing number of human diseases, including thalassemia and systemic lupus erythematosus ( 10 , 11 ). Moreover, recent studies have found that single nucleotide polymorphisms (SNPs) near the PAS can lead to changes in PAS usage and gene expression ( 12 , 13 ).…”

DPYD Exome, mRNA Expression and Uracil Levels in Early Severe Toxicity to Fluoropyrimidines: An Extreme Phenotype Approach

“…Variants in the 3′UTR may affect mRNA stability, translation efficiency, nuclear export and cellular location [ 31 ]. This variant does not seem to affect the polyadenylation signal region, one of the most sensitive places in the 3′UTR [ 32 ]. However, it may affect microRNA binding sites.…”