Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues.
Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues.
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DOI：
10.1534/genetics.116.196774
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发表时间：
2017-06
期刊：
影响因子：
3.3
通讯作者：
Mangone M
中科院分区：
文献类型：
--
作者：
Blazie SM;Geissel HC;Wilky H;Joshi R;Newbern J;Mangone M
在几乎所有的后生动物中观察到交替多聚腺苷酸化（阿帕），并导致具有不同3 '末端的mRNA同种型。这是例行的…mRNA表达动态促进和维持活生物体中体细胞组织的身份;然而，它们在这些过程中的转录后基因调控中的影响尚未完全了解。在这里，我们应用PAT-Seq方法从五个高度研究的秀丽隐杆线虫体组织中系统地分离、测序和映射组织特异性mRNA：GABA能和NMDA神经元、拱廊和肠瓣膜细胞、缝细胞和皮下组织，并研究了它们的mRNA表达动态。这些数据集与先前描述的肠、咽和身体肌肉组织的转录组的整合，精确地为所有注释的C.线虫的蛋白质编码基因，为科学界提供了重要的资源。在所有8个体细胞组织中的15，956个独特的高质量组织特异性polyA位点的定位揭示了广泛的组织特异性3′非翻译区（3′UTR）异构体通过选择性聚腺苷酸化（阿帕）转换。几乎所有广泛转录的基因都使用阿帕并在其3′ UTR中携带miRNA靶点，这些靶点通常以组织特异性方式丢失，这表明广泛使用通过阿帕调节的转录后基因调控来微调组织特异性蛋白质表达。在这个库中，人类疾病基因C。elegans orthologs rack-1和tct-1使用阿帕转换为较短的3′UTR同种型，以逃避身体肌肉组织中的miRNA调控，从而增加身体肌肉正常功能所需的蛋白质表达。我们的研究结果突出了阿帕的主要积极调控作用，允许基因在组织特异性基础上抵消miRNA调控。
Alternative polyadenylation (APA) is observed in virtually all metazoans and results in mRNA isoforms with different 3’ends. It is routinely... mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3′untranslated region (3′UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3′UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3′UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis.