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Viral and cellular N6-methyladenosine and N6,2′-O-dimethyladenosine epitranscriptomes in the KSHV life cycle

Nature Microbiologyvolume 3pages108120 (2018) | Download Citation

Abstract

N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) modifications (m6A/m) of messenger RNA mediate diverse cellular functions. Oncogenic Kaposi’s sarcoma-associated herpesvirus (KSHV) has latent and lytic replication phases that are essential for the development of KSHV-associated cancers. To date, the role of m6A/m in KSHV replication and tumorigenesis is unclear. Here, we provide mechanistic insights by examining the viral and cellular m6A/m epitranscriptomes during KSHV latent and lytic infection. KSHV transcripts contain abundant m6A/m modifications during latent and lytic replication, and these modifications are highly conserved among different cell types and infection systems. Knockdown of YTHDF2 enhanced lytic replication by impeding KSHV RNA degradation. YTHDF2 binds to viral transcripts and differentially mediates their stability. KSHV latent infection induces 5′ untranslated region (UTR) hypomethylation and 3′UTR hypermethylation of the cellular epitranscriptome, regulating oncogenic and epithelial-mesenchymal transition pathways. KSHV lytic replication induces dynamic reprogramming of epitranscriptome, regulating pathways that control lytic replication. These results reveal a critical role of m6A/m modifications in KSHV lifecycle and provide rich resources for future investigations.

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Acknowledgements

We thank S.-J.G.’s laboratory for technical assistance and helpful discussions. This work was supported by grants from the NIH (CA096512, CA124332, CA132637, CA213275, CA177377, DE025465 and CA197153) to S.-J.G., and (GM113245) to Y.H.

Author information

Author notes

  1. Hui Liu and Songyao Zhang contributed equally to this work.

Affiliations

  1. Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

    • Brandon Tan
    • , Hui Liu
    • , Suzane Ramos da Silva
    • , Hongfeng Yuan
    • , Océane Sorel
    •  & Shou-Jiang Gao
  2. School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, China

    • Hui Liu
    •  & Lin Zhang
  3. Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX, USA

    • Songyao Zhang
    • , Lin Zhang
    • , Xiaodong Cui
    •  & Yufei Huang
  4. School of Automation, Northwestern Polytechnic University, Xi’an, Shaanxi, China

    • Songyao Zhang
    •  & Shao-Wu Zhang
  5. Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu, China

    • Jia Meng
  6. Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China

    • Shou-Jiang Gao

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Contributions

Conceptualization, B.T., H.L., Y.H., S.-J.G.; investigation, B.T., S.R.D.S., O.S., H.Y.; methodology, B.T., H.L., S.Z., Y.H., S.-J.G.; formal analysis, H.L., S.Z., L.Z., J.M., X.C., S.-W.Z., Y.H.; writing—original draft, B.T., H.L., S.-J.G.; writing—review and editing, B.T., H.L., S.Z., S.R.D.S., L.Z., J.M., X.C., O.S., H.Y., S.-W.Z., Y.H., S.-J.G.; supervision and management, Y.H., S.-J.G.; funding acquisition, Y.H., S.-J.G.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Yufei Huang or Shou-Jiang Gao.

Electronic supplementary material

  1. Supplementary Information

    Supplementary Figures 1–10, Supplementary Tables 3 and 8.

  2. Life Sciences Reporting Summary

  3. Supplementary Table 1

    Latent KSHV m6A/m peaks in five types of cells latently infected by KSHV.

  4. Supplementary Table 2

    Latent and lytic KSHV m6A/m peaks in KiSLK and BCBL1-R cells.

  5. Supplementary Table 4

    Differential cellular methylation and gene expression in uninfected cells and cells latently infected by KSHV.

  6. Supplementary Table 5

    Significantly enriched pathways of hypomethylated and hypermethylated cellular genes following latent KSHV infection.

  7. Supplementary Table 6

    Differential cellular methylation and gene expression in KSHV-infected cells induced for lytic replication for 48 h compared to uninduced cells in KiSLK and BCBL1-R cells.

  8. Supplementary Table 7

    Significantly enriched pathways of 5′ UTR hypomethylated and 3′ UTR hypermethylated cellular genes in KSHV-infected cells induced for lytic replication for 48 h compared to uninduced cells in KiSLK and BCBL1-R cells.

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DOI

https://doi.org/10.1038/s41564-017-0056-8