Molecular cloning and characterization of APOBEC3 family in tree shrew

Luo, Meng; Yu, Fan; Mu, Dan; Yao, Yong‐Gang; Zheng, Yong‐Tang

doi:10.1016/j.gene.2017.12.060

Cited by 6 publications

(11 citation statements)

References 52 publications

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“… 9 Primary tree shrew hepatocytes (PTHs) are susceptible to HBV infection 1 , 4 and can respond to IFN-ɑ treatment in vitro. 8 In the current study, treatment of PTHs with IFN-ɑ controlled HBV covalently closed circular DNA (cccDNA) which was as efficient as treatment with the nucleoside analog lamivudine (LAM, 3TC) (Fig. 1a ).…”

mentioning

confidence: 65%

“…Cytidine deamination of HBV DNA by tsA3Z1a and tsA3Z2a-2b was strong (Fig. 1g ), which may be correlated with localization of these proteins in the nucleus, 8 where they can gain access to cccDNA. Interestingly, tsA3Z3 exhibited weak hypermutation ability, but it had anti-HBsAg/HBeAg activity in the culture supernatant.…”

mentioning

confidence: 86%

“… 5 In primary liver cultures of HBV-infected tree shrews, the HBV genome-editing profiles with G to A hypermutation are similar to those observed in humans. 6 We previously annotated tree shrew genome sequences 7 and identified the tree shrew (ts) APOBEC3 family, 8 thus revealing the existence of APOBEC3 factors in tree shrews, as well as interactions between tsAPOBEC3 and HBV.…”

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confidence: 99%

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The tsAPOBEC3 proteins restrict HBV replication and may limit the establishment of persistent infection in tree shrews

Luo

Zheng

2020

Cell Mol Immunol

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confidence: 65%

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confidence: 86%

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confidence: 99%

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The tsAPOBEC3 proteins restrict HBV replication and may limit the establishment of persistent infection in tree shrews

Luo

Zheng

2020

Cell Mol Immunol

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“…We verified the accuracy of the TS_3.0 transcripts by comparing the annotated transcripts with those characterized by molecular cloning. In total, 30 transcripts reported in our previous studies ( Gu et al, 2019a ; Luo et al, 2018 ; Yao et al, 2019 ; Yu et al, 2014 , 2016 ) (Supplementary Table S4) were selected for comparison using blastall (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download). An E-value<1e-5 was used as a cutoff to define whether a transcript obtained by molecular cloning was included in the TS_3.0 genome annotation.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

Zhang

et al. 2021

Zoological Research

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The Chinese tree shrew ( Tupaia belangeri chinensis ) is emerging as an important experimental animal in multiple fields of biomedical research. Comprehensive reference genome annotation for both mRNA and long non-coding RNA (lncRNA) is crucial for developing animal models using this species. In the current study, we collected a total of 234 high-quality RNA sequencing (RNA-seq) datasets and two long-read isoform sequencing (ISO-seq) datasets and improved the annotation of our previously assembled high-quality chromosome-level tree shrew genome. We obtained a total of 3 514 newly annotated coding genes and 50 576 lncRNA genes. We also characterized the tissue-specific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome. We identified 144 tree shrew-specific gene families, including interleukin 6 ( IL6 ) and STT3 oligosaccharyltransferase complex catalytic subunit B ( STT3B ), which underwent significant changes in size. Comparison of the overall expression patterns in tissues and pathways across four species (human, rhesus monkey, tree shrew, and mouse) indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level. Notably, the newly annotated purine rich element binding protein A ( PURA ) gene and the STT3B gene family showed dysregulation upon viral infection. The updated version of the tree shrew genome annotation (KIZ version 3: TS_3.0) is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.

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“…Therefore, the findings of the study discovered APOBEC3 proteins as a barrier to HIV-1 infection; this information is critical for developing gene-edited tree shrew HIV-1-infected models. Previously, induction of hypermutations in the HIV-1 genome by APOBEC3 proteins was reported [ 79 ].…”

Section: Tree Shrew Model For Other Human Virusesmentioning

confidence: 99%

Tree Shrew as an Emerging Small Animal Model for Human Viral Infection: A Recent Overview

Kayesh

Sanada

Kohara

et al. 2021

Viruses

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Viral infection is a global public health threat causing millions of deaths. A suitable small animal model is essential for viral pathogenesis and host response studies that could be used in antiviral and vaccine development. The tree shrew (Tupaia belangeri or Tupaia belangeri chinenesis), a squirrel-like non-primate small mammal in the Tupaiidae family, has been reported to be susceptible to important human viral pathogens, including hepatitis viruses (e.g., HBV, HCV), respiratory viruses (influenza viruses, SARS-CoV-2, human adenovirus B), arboviruses (Zika virus and dengue virus), and other viruses (e.g., herpes simplex virus, etc.). The pathogenesis of these viruses is not fully understood due to the lack of an economically feasible suitable small animal model mimicking natural infection of human diseases. The tree shrew model significantly contributes towards a better understanding of the infection and pathogenesis of these important human pathogens, highlighting its potential to be used as a viable viral infection model of human viruses. Therefore, in this review, we summarize updates regarding human viral infection in the tree shrew model, which highlights the potential of the tree shrew to be utilized for human viral infection and pathogenesis studies.

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Molecular cloning and characterization of APOBEC3 family in tree shrew

Cited by 6 publications

References 52 publications

The tsAPOBEC3 proteins restrict HBV replication and may limit the establishment of persistent infection in tree shrews

The tsAPOBEC3 proteins restrict HBV replication and may limit the establishment of persistent infection in tree shrews

Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

Tree Shrew as an Emerging Small Animal Model for Human Viral Infection: A Recent Overview

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