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Volume 36 Issue 2
April 2021

    Lijia Jia, Jianjun Chen, Haizhou Liu, Wenhui Fan, Depeng Wang, Jing Li and Di Liu. Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain[J]. Virologica Sinica, 2021, 36(2): 321-324. doi: 10.1007/s12250-020-00217-2
    Citation: Lijia Jia, Jianjun Chen, Haizhou Liu, Wenhui Fan, Depeng Wang, Jing Li, Di Liu. Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain .VIROLOGICA SINICA, 2021, 36(2) : 321-324.  http://dx.doi.org/10.1007/s12250-020-00217-2
    shu

    中国非洲猪瘟病毒株基因组中潜在的m6A和m5C甲基化

    • 1.

      中国科学院武汉病毒研究所

    • 通讯作者： 李晶, lj418@163.com, ORCID: http://orcid.org/0000-0001-9588-5291
      ; 刘翟, liud@wh.iov.cn, ORCID: http://orcid.org/0000-0003-3693-2726
    • 收稿日期： 2020-01-05
      录用日期： 2020-03-07
      出版日期： 2020-04-08

    • 2018年8月非洲猪瘟首次传入中国，这种流行病在短短几个月内就席卷了全国，并继续传播到蒙古和越南等东亚国家。非洲猪瘟病毒基因组十分复杂，目前已知的信息严重不足，故深化ASFV基因组学研究十分必要。本研究首次利用纳米孔测序技术来检测临床样本中非洲猪瘟病毒基因组内的甲基化修饰，并使用无监督学习方法鉴定了基因II型ASFV的m5C和m6A甲基化修饰潜在位点，从表观遗传学的层面为病毒-宿主相互作用提供了新的思路，也为表观修饰图谱绘制的后续工作奠定了基础。

    Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain

    • 1.

      CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China

    • 2.

      Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China

    • 3.

      African Swine Fever Regional Laboratory of China, Wuhan 430071, China

    • 4.

      CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

    • 5.

      NextOmics Biosciences, Wuhan 430074, China

    • 6.

      Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China

    • 7.

      University of Chinese Academy of Sciences, Beijing 100049, China

    • Corresponding author: Jing Li, lj418@163.com Di Liu, liud@wh.iov.cn
    • ORCID: http://orcid.org/0000-0001-9588-5291; http://orcid.org/0000-0003-3693-2726
    • Received Date: 05 January 2020
      Accepted Date: 07 March 2020
      Published Date: 08 April 2020
    • 加载中

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          doi: 10.1111/tbed.13124

      3. Cackett G, Matelska D, Sykora M, Portugal R, Malecki M, Bahler J, Dixon L, Werner F (2019) Temporal transcriptome and promoter architecture of the African swine fever virus bioRxiv. https://doi.org/10.1101/847343

      4. China News Service (2019) China's Ministry of Agriculture and Rural Affairs: 1.193 million pigs have been killed due to African swine fever. https://www.chinanews.com/gn/2019/11-22/9014851.shtml

      5. Galindo I, Alonso C (2017) African swine fever virus: a review. Viruses 9:103–112
          doi: 10.3390/v9050103

      6. Gallardo MC, Reoyo AT, Fernández-Pinero J, Iglesias I, Muñoz MJ, Arias ML (2015) African swine fever: a global view of the current challenge. Porcine Health Manag 1:21
          doi: 10.1186/s40813-015-0013-y

      7. Gokhale NS, McIntyre ABR, Mattocks MD, Holley CL, Lazear HM, Mason CE, Horner SM (2020) Altered m6A modification of specific cellular transcripts affects flaviviridae. Infect Mol Cell 77:542–555 e548
          doi: 10.1016/j.molcel.2019.11.007

      8. Gouil Q, Keniry A (2019) Latest techniques to study DNA methylation. Essays Biochem 63:639–648
          doi: 10.1042/EBC20190027

      9. Hoelzer K, Shackelton LA, Parrish CR (2008) Presence and role of cytosine methylation in DNA viruses of animals. Nucleic Acids Res 36:2825–2837
          doi: 10.1093/nar/gkn121

      10. Jia L, Jiang M, Wu K, Hu J, Wang Y, Quan W, Hao M, Liu H, Wei H, Fan W, Liu W, Hu R, Wang D, Li J, Chen J, Liu D (2019) Nanopore sequencing of African swine fever virus. Sci China Life Sci 63:160–164

      11. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760
          doi: 10.1093/bioinformatics/btp324

      12. Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K (2019) Detection of DNA base modifications by deep recurrent neural network on Oxford nanopore sequencing data. Nat Commun 10:2449
          doi: 10.1038/s41467-019-10168-2

      13. Salas ML, Kuznar J, Viñuela E (1981) Polyadenylation, methylation, and capping of the RNA synthesized in vitro by African swine fever virus. Virology 113:484–491
          doi: 10.1016/0042-6822(81)90176-8

      14. Senol Cali D, Kim JS, Ghose S, Alkan C, Mutlu O (2019) Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Brief Bioinform 20:1542–1559

      15. Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W (2017) Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods 14:407

      16. Stoiber M, Quick J, Egan R, Eun LJ, Celniker S, Neely RK, Loman N, Pennacchio L, Brown J (2017) De novo identification of DNA modifications enabled by genome-guided nanopore signal processing. bioRxiv. https://doi.org/10.1101/094672

      17. Wang Z, Jia L, Li J, Liu H, Liu D (2019) Pan-genomic analysis of African swine fever virus. Virol Sin. https://doi.org/10.1007/s12250-019-00173-6

      18. Weber S, Hakobyan A, Zakaryan H, Doerfler W (2018) Intracellular African swine fever virus DNA remains unmethylated in infected Vero cells. Epigenomics 10:289–299

      19. Wen X, He X, Zhang X, Zhang XF, Liu L, Guan Y, Zhang Y, Bu Z (2019) Genome sequences derived from pig and dried blood pig feed samples provide important insights into the transmission of African swine fever virus in China in 2018. Emerg Microbes Infect 8:303–306

    • 加载中

    • Electronic Supplementary Material

      10.1007s12250-020-00217-2-ESM2.xlsx
      10.1007s12250-020-00217-2-ESM1.pdf
      10.1007s12250-020-00217-2-ESM1.xlsx
      10.1007s12250-020-00217-2-ESM1.pdf

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      Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain

        Corresponding author: Jing Li, lj418@163.com
        Corresponding author: Di Liu, liud@wh.iov.cn
      • 1. CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
      • 2. Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
      • 3. African Swine Fever Regional Laboratory of China, Wuhan 430071, China
      • 4. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
      • 5. NextOmics Biosciences, Wuhan 430074, China
      • 6. Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
      • 7. University of Chinese Academy of Sciences, Beijing 100049, China
      • Received Date: 05 January 2020
      • Accepted Date: 07 March 2020
      • Published Date: 08 April 2020

      Abstract: 

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