Premium
In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis
Author(s) -
Lin Weimin,
Xu Hao,
Wu Yunshu,
Wang Jun,
Yuan Quan
Publication year - 2020
Publication title -
journal of cellular physiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.529
H-Index - 174
eISSN - 1097-4652
pISSN - 0021-9541
DOI - 10.1002/jcp.29005
Subject(s) - single nucleotide polymorphism , expression quantitative trait loci , biology , genetics , in silico , snp , gene , n6 methyladenosine , methylation , genotype , methyltransferase
Genetic variation is considered to affect the N 6 ‐methyladenosine (m6A) RNA transcript modification, which is the most prevalent posttranscriptional messenger RNA modification. This study aimed to identify m6A‐associated single‐nucleotide polymorphisms (m6A‐SNPs) that may affect m6A methylation from numerous periodontitis (PD) SNPs. We identified an abundance of m6A‐SNPs by analyzing raw data of published PD genome‐wide association studies and m6A‐SNPs list from the m6AVar database. Other evidence was found in public databases for expression quantitative trait loci (eQTL) and differential gene expression analysis. Accordingly, 1938 m6A‐SNPs were identified, 104 of which appeared to be associated with PD ( p < .05) while 65 showed eQTL signals. Lastly, the leading SNP rs2723183 ( p = 3.93E−07) was predicted to regulate local gene IL‐37 expression in PD ( p = 2.64E−05; in GSE10334) and change regulatory motif RXRA. In summary, dozens of PD‐associated m6A‐SNPs were identified and their possible functions were demonstrated in this study.