期刊
BMC GENOMICS
卷 23, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s12864-022-08405-y
关键词
Expression quantitative trait loci (eQTLs); RNA-Seq; mRNA stability; Stability QTLs (stQTLs)
资金
- Cancer Prevention Research Institute of Texas (CPRIT) [RR180061]
- National Cancer Institute of the National Institutes of Health [1R21CA227996, U19CA203654]
In this study, a computational framework was proposed to infer mRNA stability of genes using RNA-seq data and identify stQTLs. The results revealed that stQTLs were enriched in the CDS and 3'UTR regions, while eQTLs were enriched in multiple regions. Additionally, stQTLs were more likely to overlap with RNA binding protein and microRNA binding sites. This study demonstrates that simultaneous identification of stQTLs and eQTLs provides more mechanistic insight into the association between genetic variants and gene expression levels.
Background Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs). Results Here, we presented a computational framework that takes advantage of recently developed methods to infer the mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3942 genes and 186,132 eQTLs for 4751 genes from 15,122,700 genetic variants for 13,476 genes on the autosomes, respectively. Interestingly, our results indicated that stQTLs were enriched in the CDS and 3'UTR regions, while eQTLs are enriched in the CDS, 3'UTR, 5'UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据