Quantitative Proteomics, Institute of Molecular Biology, Mainz 55128, Germany.
Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
Nucleic Acids Res. 2020 Jun 19;48(11):5926-5938. doi: 10.1093/nar/gkaa359.
Alternative polyadenylation (APA) produces isoforms with distinct 3'-ends, yet their functional differences remain largely unknown. Here, we introduce the APA-seq method to detect the expression levels of APA isoforms from 3'-end RNA-Seq data by exploiting both paired-end reads for gene isoform identification and quantification. We detected the expression levels of APA isoforms in individual Caenorhabditis elegans embryos at different stages throughout embryogenesis. Examining the correlation between the temporal profiles of isoforms led us to distinguish two classes of genes: those with highly correlated isoforms (HCI) and those with lowly correlated isoforms (LCI) across time. We hypothesized that variants with similar expression profiles may be the product of biological noise, while the LCI variants may be under tighter selection and consequently their distinct 3' UTR isoforms are more likely to have functional consequences. Supporting this notion, we found that LCI genes have significantly more miRNA binding sites, more correlated expression profiles with those of their targeting miRNAs and a relative lack of correspondence between their transcription and protein abundances. Collectively, our results suggest that a lack of coherence among the regulation of 3' UTR isoforms is a proxy for selective pressures acting upon APA usage and consequently for their functional relevance.
可变多聚腺苷酸化（APA）产生具有不同 3' 端的异构体，但它们的功能差异在很大程度上仍然未知。在这里，我们引入了 APA-seq 方法，通过利用双端reads 来识别和定量基因异构体，从 3' 端 RNA-Seq 数据中检测 APA 异构体的表达水平。我们在个体秀丽隐杆线虫胚胎的不同发育阶段检测了 APA 异构体的表达水平。检查异构体的时间曲线之间的相关性，使我们能够区分两类基因：在整个胚胎发生过程中具有高度相关异构体（HCI）和低度相关异构体（LCI）的基因。我们假设具有相似表达谱的变体可能是生物噪声的产物，而 LCI 变体可能受到更严格的选择，因此其独特的 3' UTR 异构体更有可能具有功能后果。支持这一观点，我们发现 LCI 基因具有更多的 miRNA 结合位点，与其靶向 miRNA 的表达谱更相关，并且其转录和蛋白质丰度之间的对应关系相对较少。总的来说，我们的结果表明，3' UTR 异构体调控之间缺乏一致性是 APA 使用受到选择压力的代理，因此也是其功能相关性的代理。
