Alternative polyadenylation produces multiple 3\u2019 untranslated regions of odorant receptor mRNAs in mouse olfactory sensory neurons

Mohamed Doulazmi,Caroline Dubacq,Alain Trembleau,Cyril Cros,Isabelle Dusart

doi:10.1186/s12864-019-5927-3

Abstract

BackgroundOdorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterization of their mRNA 3′ untranslated regions (3’UTRs). Given the increasing importance of UTRs in the understanding of RNA metabolism, and the growing interest in alternative polyadenylation especially in the nervous system, we aimed at identifying the alternative isoforms of odorant receptor mRNAs generated through 3’UTR variation.ResultsWe implemented a dedicated pipeline using IsoSCM instead of Cufflinks to analyze RNA-Seq data from whole olfactory mucosa of adult mice and obtained an extensive description of the 3’UTR isoforms of odorant receptor mRNAs. To validate our bioinformatics approach, we exhaustively analyzed the 3’UTR isoforms produced from 2 pilot genes, using molecular approaches including northern blot and RNA ligation mediated polyadenylation test. Comparison between datasets further validated the pipeline and confirmed the alternative polyadenylation patterns of odorant receptors. Qualitative and quantitative analyses of the annotated 3′ regions demonstrate that 1) Odorant receptor 3’UTRs are longer than previously described in the literature; 2) More than 77% of odorant receptor mRNAs are subject to alternative polyadenylation, hence generating at least 2 detectable 3’UTR isoforms; 3) Splicing events in 3’UTRs are restricted to a limited subset of odorant receptor genes; and 4) Comparison between male and female data shows no sex-specific differences in odorant receptor 3’UTR isoforms.ConclusionsWe demonstrated for the first time that odorant receptor genes are extensively subject to alternative polyadenylation. This ground-breaking change to the landscape of 3’UTR isoforms of Olfr mRNAs opens new avenues for investigating their respective functions, especially during the differentiation of olfactory sensory neurons.

Highlights

Odorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterization of their mRNA 3′ untranslated regions (3’UTRs)
To document the 3’UTRs of Olfr mRNAs in the mouse, and to determine to what extent these mRNAs are subject to alternative polyadenylation (APA), we developed a dedicated strategy based on computational analyses of previously published RNA-Seq datasets obtained from adult mouse whole olfactory mucosa [26, 40]
We further showed that 3’UTRs of Olfr mRNAs are rarely subject to alternative or optional splicing, an observation in line with the very low number of exons detected in the STAR output in the 3’UTRs of Olfr mRNAs (Additional file 6: Table S3)

Summary

Introduction

Odorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterization of their mRNA 3′ untranslated regions (3’UTRs). In terms of projections, it was shown that all OSNs expressing a given Olfr gene are scattered in large zones of the OM, but that their axons converge onto a small number of glomeruli [6,7,8]. In addition to their role as chemoreceptors, ORs are involved in these two processes: ORs ensure their own monogenic and monoallelic expression [9], and play a critical role in guiding OSN axons towards their appropriate glomeruli [10,11,12,13]. Given the triple role played by Olfr genes in OSNs, and in view of deciphering the molecular and cellular mechanisms involved in these different functions, it is critical to fully characterize their structure and expression

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Discussion

Conclusion