Genome-wide evolution analysis reveals low CpG contents of fast-evolving genes and identifies antiviral microRNAs  

作　　者：Wenhong Zu Hang Zhang Xun Lan Xu Tan 

机构地区：[1]MOE Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical Biology,School of Pharmaceutical Sciences,Tsinghua University,Beijing,100084,China [2]Beijing Advanced Innovation Center for Structural Biology.Beijing Frontier Research Center for Biological Structures,Tsinghua University,Beijing,100084,China [3]Department of Basic Medical Sciences,School of Medicine,Tsinghua University,Beijing,100084,China [4]Center for Infectious Disease Research,Tsinghua University,Beijing,100084,China [5]Tsinghua-Peking Center for Life Sciences,Beijing,100084,China

出　　处：《Journal of Genetics and Genomics》2020年第1期49-60,共12页遗传学报（英文版）

基　　金：supported by the National Natural Science Foundation of China (Grant No. 31670777);the China National Funds for Distinguished Young Scientists (Grant No. 31722030);the Beijing Advanced Innovation Center for Structural Biology to X.T.;the Tsinghua-Peking Joint Center for Life Sciences (Grant No. 61020100119);the National Thousand Young Talents Program of China (Grant No. 042021011) to X.L.

摘　　要：Noncoding RNAs(ncRNAs) play important roles in many biological processes and provide materials for evolutionary adaptations beyond protein-coding genes, such as in the arms race between the host and pathogen. However, currently, a comprehensive high-resolution analysis of primate genomes that includes the latest annotated ncRNAs is not available. Here, we developed a computational pipeline to estimate the selections that act on noncoding regions based on comparisons with a large number of reference sequences in introns adjacent to the interested regions. Our method yields result comparable with those of the established codon-based method and phyloP method for coding genes;thus, it provides a holistic framework for estimating the selection on the entire genome. We further showed that fastevolving protein-coding genes and their corresponding 50 UTRs have a significantly lower frequency of the CpG dinucleotides than those evolving at an average pace, and these fast-evolving genes are enriched in the process of immunity and host defense. We also identified fast-evolving miRNAs with antiviral functions in cells. Our results provide a resource for high-resolution evolution analysis of the primate genomes.Noncoding RNAs(ncRNAs) play important roles in many biological processes and provide materials for evolutionary adaptations beyond protein-coding genes, such as in the arms race between the host and pathogen. However, currently, a comprehensive high-resolution analysis of primate genomes that includes the latest annotated ncRNAs is not available. Here, we developed a computational pipeline to estimate the selections that act on noncoding regions based on comparisons with a large number of reference sequences in introns adjacent to the interested regions. Our method yields result comparable with those of the established codon-based method and phyloP method for coding genes; thus, it provides a holistic framework for estimating the selection on the entire genome. We further showed that fastevolving protein-coding genes and their corresponding 50 UTRs have a significantly lower frequency of the CpG dinucleotides than those evolving at an average pace, and these fast-evolving genes are enriched in the process of immunity and host defense. We also identified fast-evolving miRNAs with antiviral functions in cells. Our results provide a resource for high-resolution evolution analysis of the primate genomes.

关 键 词：Host-virus interaction Positive selection CPG DINUCLEOTIDE Noncoding RNA MicroRNA 

分 类 号：R373[医药卫生—病原生物学]