Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m^6A Modification

作     者：Yuan Zhou Qinghua Cui 

作者机构：Department of Biomedical Informatics School of Basic Medical Sciences Peking University 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2018年第16卷第2期

页      面：127-135页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 1001[医学-基础医学(可授医学、理学学位)] 071007[理学-遗传学] 0714[理学-统计学（可授理学、经济学学位）] 0703[理学-化学] 0701[理学-数学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

基　　金：supported by the National Natural Science Foundation of China (Grant Nos. 81670462 and 81422006 to QC) China Postdoctoral Science Foundation (Grant No. 2016M591024 to YZ) 

主　　题：m^6A Epitranscriptome Signaling network Gene expression regulation Gene importance 

摘      要：The m^6A modification has been implicated as an important epitranscriptomic marker, which plays extensive roles in the regulation of transcript stability, splicing, translation, and localization. Nevertheless, only some genes are repeatedly modified across various conditions and the principle of m^6A regulation remains elusive. In this study, we performed a systems-level analysis of human genes frequently regulated by m^6A modification （m^6Afreq genes） and those occasionally regulated by m^6A modification （m^6Aocca genes）. Compared to the m^6Aocca genes, the m^6Afreq genes exhibit gene importance-related features, such as lower dN/dS ratio, higher protein-protein interaction network degree, and reduced tissue expression specificity. Signaling network analysis indicates that the m^6Afreq genes are associated with downstream components of signaling cascades, high-linked signaling adaptors, and specific network motifs like incoherent feed forward loops. Moreover, functional enrichment analysis indicates significant overlaps between the m^6Afreq genes and genes involved in various layers of gene expression, such as being the microRNA targets and the regulators of RNA processing. Therefore, our findings suggest the potential interplay between m^6A epitranscriptomic regulation and other gene expression regulatory machineries.