Longitudinal RNA-Seq Analysis of the Repeatability of Gene Expression and Splicing in Human Platelets Identifies a Platelet SELP Splice QTL
Longitudinal RNA-Seq Analysis of the Repeatability of Gene Expression and Splicing in Human Platelets Identifies a Platelet SELP Splice QTL
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DOI：
10.1161/circresaha.119.315215
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发表时间：
2020-02-14
影响因子：
20.1
通讯作者：
Rowley, Jesse W.
中科院分区：
文献类型：
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作者：
Rondina, Matthew T.;Voora, Deepak;Rowley, Jesse W.
基本原理：需要进行纵向研究以区分基因表达的个体内变异和个体间变异以及重复性。它们具有独特的优势，可以从环境噪声中破译遗传信号，并有可能应用于基因变异和表达研究。然而，在健康个体的基因表达的纵向分析，特别是关于选择性剪接是缺乏最主要的细胞类型，包括platelet.Objective：为了评估血小板的基因表达和剪接的可重复性，并使用可重复性，以确定新的血小板表达的数量性状位点（QTLs）和剪接QTLs.Methods和结果：我们测序的转录组的血小板分离重复4年从健康个体。我们研究了血小板RNA表达和外显子跳跃（一种容易测量的选择性剪接事件）的个体内和个体间变异和重复性。我们发现，血小板基因表达一般是稳定的个体之间和个体内随着时间的推移，除了一个子集的基因丰富的炎症基因本体论。我们显示了与遗传性状相关的可重复基因的富集，包括已知的和新的血小板表达QTL。几个外显子跳跃事件也是高度可重复的，这表明血小板中的剪接模式是可遗传的。其中最可重复的是SELP的外显子14跳读。因此，我们确定rs6128作为血小板剪接QTL，并定义了rs6128依赖SELP外显子14跳跃和种族之间的关联。体外实验表明，这种单核苷酸变异直接影响外显子14跳跃和改变跨膜与可溶性P-选择素蛋白production.Conclusions的比例：我们得出结论，血小板转录组一般是稳定的超过4年。我们展示了使用基因表达和剪接的重复性来鉴定新的血小板表达QTL和剪接QTL。rs6128是血小板剪接QTL，其改变SELP外显子14跳跃和可溶性与跨膜P-选择素蛋白产生。
Rationale:Longitudinal studies are required to distinguish within versus between-individual variation and repeatability of gene expression. They are uniquely positioned to decipher genetic signal from environmental noise, with potential application to gene variant and expression studies. However, longitudinal analyses of gene expression in healthy individuals-especially with regards to alternative splicing-are lacking for most primary cell types, including platelets.Objective:To assess repeatability of gene expression and splicing in platelets and use repeatability to identify novel platelet expression quantitative trait loci (QTLs) and splice QTLs.Methods and Results:We sequenced the transcriptome of platelets isolated repeatedly up to 4 years from healthy individuals. We examined within and between individual variation and repeatability of platelet RNA expression and exon skipping, a readily measured alternative splicing event. We find that platelet gene expression is generally stable between and within-individuals over time-with the exception of a subset of genes enriched for the inflammation gene ontology. We show an enrichment among repeatable genes for associations with heritable traits, including known and novel platelet expression QTLs. Several exon skipping events were also highly repeatable, suggesting heritable patterns of splicing in platelets. One of the most repeatable was exon 14 skipping of SELP. Accordingly, we identify rs6128 as a platelet splice QTL and define an rs6128-dependent association between SELP exon 14 skipping and race. In vitro experiments demonstrate that this single nucleotide variant directly affects exon 14 skipping and changes the ratio of transmembrane versus soluble P-selectin protein production.Conclusions:We conclude that the platelet transcriptome is generally stable over 4 years. We demonstrate the use of repeatability of gene expression and splicing to identify novel platelet expression QTLs and splice QTLs. rs6128 is a platelet splice QTL that alters SELP exon 14 skipping and soluble versus transmembrane P-selectin protein production.