Genetic Variants Associated MRNA Stability in Lung

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2022 Mar 11

PMID 35272635

Authors

Jian-Rong Li

Mabel Tang

Yafang Li

Christopher I Amos

Chao Cheng

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective.

Zhu Z, Chen X, Zhang S, Yu R, Qi C, Cheng L Hum Genet. 2023; 142(11):1543-1560.

PMID: 37755483 DOI: 10.1007/s00439-023-02602-9.

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