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.
Electronic supplementary material
Supplementary Figures 1–10, Supplementary Tables 3 and 8.
Latent KSHV m6A/m peaks in five types of cells latently infected by KSHV.
Latent and lytic KSHV m6A/m peaks in KiSLK and BCBL1-R cells.
Differential cellular methylation and gene expression in uninfected cells and cells latently infected by KSHV.
Significantly enriched pathways of hypomethylated and hypermethylated cellular genes following latent KSHV infection.
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.
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.