CNRS, Institut de Biologie Paris Seine, Biological adaptation and ageing, B2A, Sorbonne Université, F-75005, Paris, France.
CNRS, INSERM, Institut de Biologie Paris Seine, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005, Paris, France.
BMC Genomics. 2019 Jul 12;20(1):577. doi: 10.1186/s12864-019-5927-3.
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). 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.
We 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.
We 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.
气味受体基因构成了哺乳动物基因组中最大的基因家族，该家族在多个物种中得到了广泛研究，但迄今为止，对其 mRNA 3'非翻译区（3'UTR）的特征描述关注甚少。鉴于 UTR 在理解 RNA 代谢中的重要性不断增加，以及对特别是在神经系统中的可变多聚腺苷酸化的兴趣日益浓厚，我们旨在确定通过 3'UTR 变异产生的气味受体 mRNA 的替代异构体。
我们使用 IsoSCM 而不是 Cufflinks 实施了一个专门的管道，来分析成年小鼠整个嗅黏膜的 RNA-Seq 数据，并对气味受体 mRNA 的 3'UTR 异构体进行了广泛的描述。为了验证我们的生物信息学方法，我们使用包括 northern blot 和 RNA 连接介导的多聚腺苷酸化测试在内的分子方法，对 2 个先导基因产生的 3'UTR 异构体进行了详尽的分析。数据集之间的比较进一步验证了该管道，并确认了气味受体的可变多聚腺苷酸化模式。对注释的 3'区域的定性和定量分析表明：1）气味受体 3'UTR 比文献中以前描述的要长；2）超过 77%的气味受体 mRNA 受到可变多聚腺苷酸化的影响，因此至少产生 2 种可检测的 3'UTR 异构体；3）3'UTR 中的剪接事件仅限于有限数量的气味受体基因；4）雌雄数据之间的比较表明，气味受体 3'UTR 异构体没有性别特异性差异。
我们首次证明气味受体基因广泛受到可变多聚腺苷酸化的影响。这一开创性的变化改变了 Olfr mRNA 的 3'UTR 异构体的景观，为研究它们各自的功能开辟了新的途径，特别是在嗅觉感觉神经元分化过程中。
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