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

Wenhong Zu; Hang Zhang; Xun Lan; Xu Tan

doi:10.1016/j.jgg.2019.12.001

Volume 47 Issue 1

Jan. 2020

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Article Navigation > Journal of Genetics and Genomics > 2020 > 47(1): 49-60

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

doi: 10.1016/j.jgg.2019.12.001

Wenhong Zu^{a, b},
Hang Zhang^{a, b},
Xun Lan^{c, e},
Xu Tan^{a, b, d, e}

a
MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
b
Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
c
Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
d
Center for Infectious Disease Research, Tsinghua University, Beijing, 100084, China
e
Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China

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Corresponding 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.
- Host-virus interaction,
- Positive selection,
- CpG dinucleotide,
- Noncoding RNA,
- MicroRNA

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References(124)

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