Systematic identification of functional SNPs interrupting 3'UTR polyadenylation signals.

Eldad David Shulman,Ran Elkon,Andreas Gruber

doi:10.1371/journal.pgen.1008977

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.

Highlights

The maturation of mRNA 30 ends is a 2-steps process, termed cleavage and polyadenylation, that involves endonucleolytic cleavage of the nascent RNA followed by synthesis of a poly(A) tail on the 30 terminus of the cleaved product [1]
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
As 30 UTRs contain ciselements that serve as major docking platforms for microRNAs and RNA binding proteins (RBPs), which are involved in various aspects of mRNA metabolism, 30 UTR alternative polyadenylation (APA) can affect post-transcriptional regulation in multiple ways, including the modulation of mRNA stability, translation efficiency, nuclear export and cellular localization [7,8,9]

Summary

Introduction

The maturation of mRNA 30 ends is a 2-steps process, termed cleavage and polyadenylation, that involves endonucleolytic cleavage of the nascent RNA followed by synthesis of a poly(A) tail on the 30 terminus of the cleaved product [1]. Cleavage and polyadenylation sites (p(A) sites) are determined and controlled by adjacent RNA cis-regulatory elements, the principal among them is the polyadenylation signal (PAS) AAUAAA, typically located ~20-nt upstream of the p(A) site. The majority of human proteincoding genes contain several alternative p(A) sites in their 3’UTR, making alternative polyadenylation (APA) a widespread regulatory layer that generates transcript isoforms with alternative 30 ends, and correspondingly, different 3’UTR lengths [1, 4,5,6]. As 30 UTRs contain ciselements that serve as major docking platforms for microRNAs (miRNAs) and RNA binding proteins (RBPs), which are involved in various aspects of mRNA metabolism, 30 UTR APA can affect post-transcriptional regulation in multiple ways, including the modulation of mRNA stability, translation efficiency, nuclear export and cellular localization [7,8,9]. Our current understanding of the impact of APA on gene regulation and of its biological roles is still very rudimentary

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Conclusion