Hang Zhang
Xun Lan
Xu Tan
aMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
bBeijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
cDepartment of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
dCenter for Infectious Disease Research, Tsinghua University, Beijing, 100084, China
eTsinghua-Peking Center for Life Sciences, Beijing, 100084, China
More InformationCorresponding author: E-mail address: xlan@tsinghua.edu.cn (Xun Lan);E-mail address: xutan@tsinghua.edu.cn (Xu Tan)
Publish Date:2020-01-25
Abstract
Abstract
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 fast-evolving protein-coding genes and their corresponding 5′ 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.Keywords: Host-virus interaction,
Positive selection,
CpG dinucleotide,
Noncoding RNA,
MicroRNA
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