Post-transcriptional regulation of human immunodeficiency virus type-2 (HIV-2) replication by N6-methyladenosine

Human immunodeficiency virus type-2 (HIV-2) establishes reservoirs at levels comparable to HIV-1, but its infection is associated with lower rates of progression to AIDS. As such, a hallmark of people living with HIV-2 is the very low—usually undetectable—viral loads, which is partially explained by a post-transcriptional repression exerted at the level of protein synthesis and the accumulation of the full-length RNA in cytoplasmic granules. Here, we investigated whether HIV-2 Gag expression was regulated by the presence of the m6A RNA modification. Our results indicate that the HIV-2 full-length RNA contains m6A residues, which are required for Gag synthesis. Interestingly, the YTHDF family of cytoplasmic m6A readers exert different effects on HIV-2 Gag synthesis. As such, while YTHDF1 and YTHDF2 are necessary for Gag synthesis, YTHDF3 negatively regulates Gag expression by promoting full-length RNA localization in cytoplasmic granules. Interestingly, we demonstrate that the cellular m6A machinery including writers, erasers and readers re-localize into cytoplasmic granules together with the full-length RNA in a non-Gag producing cell sub-population. We also observed that FTO overexpression has no effect in Gag synthesis but promotes full-length RNA packaging suggesting a dynamic regulation of the cytoplasmic fate of this viral RNA. Together, these data suggest that the HIV-2 full-length RNA undergoes a complex regulation exerted by the cellular m6A machinery that controls the cytoplasmic localization, ribosome association and particle incorporation of this viral RNA. We are providing RNAseq data from inputs (fragments of polyA RNA) and m6A-immunoprecipitated RNA from both HEK293T cells expressing HIV-2 pROD10. Two biological replicates are included.