Benoit Bouvrette Louis Philip, Cody Neal A L, Bergalet Julie, Lefebvre Fabio Alexis, Diot Cédric, Wang Xiaofeng, Blanchette Mathieu, Lécuyer Eric
Institut de Recherches Clinique de Montréal (IRCM), Montréal H2W 1R7, Canada.
Département de Biochimie, Université de Montréal, Montréal H3C 3J7, Canada.
RNA. 2018 Jan;24(1):98-113. doi: 10.1261/rna.063172.117. Epub 2017 Oct 27.
Cells are highly asymmetrical, a feature that relies on the sorting of molecular constituents, including proteins, lipids, and nucleic acids, to distinct subcellular locales. The localization of RNA molecules is an important layer of gene regulation required to modulate localized cellular activities, although its global prevalence remains unclear. We combine biochemical cell fractionation with RNA-sequencing (CeFra-seq) analysis to assess the prevalence and conservation of RNA asymmetric distribution on a transcriptome-wide scale in and human cells. This approach reveals that the majority (∼80%) of cellular RNA species are asymmetrically distributed, whether considering coding or noncoding transcript populations, in patterns that are broadly conserved evolutionarily. Notably, a large number of and human long noncoding RNAs and circular RNAs display enriched levels within specific cytoplasmic compartments, suggesting that these RNAs fulfill extra-nuclear functions. Moreover, fraction-specific mRNA populations exhibit distinctive sequence characteristics. Comparative analysis of mRNA fractionation profiles with that of their encoded proteins reveals a general lack of correlation in subcellular distribution, marked by strong cases of asymmetry. However, coincident distribution profiles are observed for mRNA/protein pairs related to a variety of functional protein modules, suggesting complex regulatory inputs of RNA localization to cellular organization.
细胞具有高度不对称性，这一特征依赖于分子成分（包括蛋白质、脂质和核酸）在不同亚细胞区域的分选。RNA分子的定位是调节局部细胞活动所需的基因调控的重要层面，尽管其在整体上的普遍性仍不清楚。我们将生化细胞分级分离与RNA测序（CeFra-seq）分析相结合，以评估RNA不对称分布在转录组范围内的普遍性和保守性，研究对象包括酵母细胞和人类细胞。该方法揭示，无论考虑编码或非编码转录本群体，大多数（约80%）细胞RNA种类均呈不对称分布，其模式在进化上广泛保守。值得注意的是，大量酵母细胞和人类的长链非编码RNA及环状RNA在特定细胞质区室中呈现富集水平，这表明这些RNA具有核外功能。此外，特定分级的mRNA群体表现出独特的序列特征。对mRNA分级分离谱与其编码蛋白质的分级分离谱进行比较分析发现，亚细胞分布总体上缺乏相关性，存在明显的不对称情况。然而，对于与各种功能蛋白模块相关的mRNA/蛋白质对，观察到了一致的分布谱，这表明RNA定位对细胞组织具有复杂的调控作用。
