Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation

Laurent F Thomas,Pål Sætrom,Roderic Guigo

doi:10.1371/journal.pcbi.1002621

Laurent F Thomas, Pål Sætrom + Show 1 more

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https://doi.org/10.1371/journal.pcbi.1002621

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Abstract

Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3′ untranslated region (UTR) lengths. Different 3′UTR lengths can give different microRNA (miRNA) regulation such that shortened transcripts have increased expression. The APA process is part of human cells' natural regulatory processes, but APA also seems to play an important role in many human diseases. Although altered APA in disease can have many causes, we reasoned that mutations in DNA elements that are important for the polyA process, such as the polyA signal and the downstream GU-rich region, can be one important mechanism. To test this hypothesis, we identified single nucleotide polymorphisms (SNPs) that can create or disrupt APA signals (APA-SNPs). By using a data-integrative approach, we show that APA-SNPs can affect 3′UTR length, miRNA regulation, and mRNA expression—both between homozygote individuals and within heterozygote individuals. Furthermore, we show that a significant fraction of the alleles that cause APA are strongly and positively linked with alleles found by genome-wide studies to be associated with disease. Our results confirm that APA-SNPs can give altered gene regulation and that APA alleles that give shortened transcripts and increased gene expression can be important hereditary causes for disease.

Highlights

In protein-coding genes, the polyadenylation process consists of cleaving the end of the 39 untranslated region (UTR) of precursor messenger RNA and adding a polyadenylation tail
When investigating the region around the transcription end site, we found that the position containing the polyA signal has a markedly decreased single nucleotide polymorphisms (SNPs) density (Fig. S2B,C), indicating that SNPs arising there could have a high functional impact
To analyse SNPs in alternative polyadenylation signals, we first identified a set of SNPs that potentially create new Alternative polyadenylation (APA) signals in 39UTRs

Summary

Introduction

In protein-coding genes, the polyadenylation process consists of cleaving the end of the 39 untranslated region (UTR) of precursor messenger RNA (pre-mRNA) and adding a polyadenylation (polyA) tail. Alternative polyadenylation (APA) can occur when several polyadenylation (polyA) signals lie in the last exon of a protein-coding gene. Many APA signals are evolutionary conserved [1], and Expressed Sequence Tag (EST) data suggest that 54% of human genes have alternative polyadenylation signals [1]. The polyA signals themselves are hexamer DNA sequences that usually lie 10 to 30 nucleotides upstream from the cleavage site [2], but a GU-rich region 20 to 40 nucleotides downstream of the cleavage site is important for the polyA-process [2]. One functional consequence of APA is transcripts with different 39UTR lengths and different microRNA (miRNA) regulation [3,4]. Shortened transcripts tend to have increased expression compared with longer transcripts, and the same expression increase can be achieved by deleting miRNA target sites in nonshortened transcripts [5]

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