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


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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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

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.

Correspondence to Yufei Huang or Shou-Jiang Gao.

Electronic supplementary material

Supplementary Information

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

Life Sciences Reporting Summary

Supplementary Table 1

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

Supplementary Table 2

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

Supplementary Table 4

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

Supplementary Table 5

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

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.

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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Further reading

Fig. 1: KSHV m6A/m epitranscriptome during viral latent infection.
Fig. 2: KSHV m6A/m epitranscriptome during viral lytic replication.
Fig. 3: Silencing of YTHDF2 enhances KSHV lytic replication.
Fig. 4: Reprogramming of cellular m6A/m epitranscriptome during KSHV latency.
Fig. 5: Reprogramming of cellular m6A/m epitranscriptome during KSHV lytic replication.