title: Positive selection of the TRIM family regulatory region in primate genomes.
abstract: Viral selection pressure has acted on restriction factors that play an important role in the innate immune system by inhibiting the replication of viruses during primate evolution. Tripartite motif-containing (TRIM) family members are some of these restriction factors. It is becoming increasingly clear that gene expression differences, rather than protein-coding regions changes, could play a vital role in the anti-retroviral immune mechanism. Increasingly, recent studies have created genome-scale catalogues of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To improve our understanding of the molecular evolution mechanism of antiviral differences between species, we leveraged 14 130 DHSs derived from 145 cell types to characterize the regulatory landscape of the TRIM region. Subsequently, we compared the alignments of the DHSs across six primates and found 375 DHSs that are conserved in non-human primates but exhibit significantly accelerated rates of evolution in the human lineage (haDHSs). Furthermore, we discovered 31 human-specific potential transcription factor motifs within haDHSs, including the KROX and SP1, that both interact with HIV-1 Importantly, the corresponding haDHS was correlated with antiviral factor TRIM23 Thus, our results suggested that some viruses may contribute, through regulatory DNA differences, to organismal evolution by mediating TRIM gene expression to escape immune surveillance.
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China.
authors.forename: Dan-Dan
authors.identifier: 0000-0002-8836-2975
authors.initials: DD
authors.lastname: He
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China.
authors.forename: Yueer
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98125, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Gittelman
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China.
authors.forename: Yabin
authors.initials: Y
authors.lastname: Jin
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China fling@scut.edu.cn.
authors.forename: Fei
authors.initials: F
authors.lastname: Ling
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98125, USA akeyj@uw.edu.
authors.forename: Akey
authors.initials: A
authors.lastname: Joshua
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D019204:GTP-Binding Proteins / Q000235:genetics; D016678:Genome; D015497:HIV-1; D006801:Humans; D011323:Primates / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid; D012641:Selection, Genetic; D000070584:Tripartite Motif Proteins / Q000235:genetics*
chemical_list: C080681:TRIM23 protein, human; D000070584:Tripartite Motif Proteins; D019204:GTP-Binding Proteins
keywords: DNase I hypersensitive sites; positive selection; primate genome; regulatory variation; tripartite motif-containing protein family