Dynamics of the human and viral m 6 A RNA methylomes during HIV-1 infection of T cells

TLDR: It is shown that viral infection triggers a massive increase in m6A in both host and viral mRNAs, which identifies a new mechanism for the control of HIV-1 replication and its interaction with the host immune system.

Abstract: N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic mRNA. Very little is known of the function of m6A in the immune system or its role in host–pathogen interactions. Here, we investigate the topology, dynamics and bidirectional influences of the viral–host RNA methylomes during HIV-1 infection of human CD4 T cells. We show that viral infection triggers a massive increase in m6A in both host and viral mRNAs. In HIV-1 mRNA, we identified 14 methylation peaks in coding and noncoding regions, splicing junctions and splicing regulatory sequences. We also identified a set of 56 human gene transcripts that were uniquely methylated in HIV-1-infected T cells and were enriched for functions in viral gene expression. The functional relevance of m6A for viral replication was demonstrated by silencing of the m6A writer or the eraser enzymes, which decreased or increased HIV-1 replication, respectively. Furthermore, methylation of two conserved adenosines in the stem loop II region of HIV-1 Rev response element (RRE) RNA enhanced binding of HIV-1 Rev protein to the RRE in vivo and influenced nuclear export of RNA. Our results identify a new mechanism for the control of HIV-1 replication and its interaction with the host immune system. Infection with HIV-1 triggers an increase in N6-methyladenosine (m6A) modification of both viral and host mRNAs, which impacts viral replication and nuclear export of viral RNA.