Epitranscriptomic addition of m(6)A regulates HIV-1 RNA stability and alternative splicing

Previous work has demonstrated that the epitranscriptomic addition of m(6)A to viral transcripts can promote the replication and pathogenicity of a wide range of DNA and RNA viruses, including HIV-1, yet the underlying mechanisms responsible for this effect have remained unclear. It is known that m(6)A function is largely mediated by cellular m(6)A binding proteins or readers, yet how these regulate viral gene expression in general, and HIV-1 gene expression in particular, has been controversial. Here, we confirm that m(6)A addition indeed regulates HIV-1 RNA expression and demonstrate that this effect is largely mediated by the nuclear m(6)A reader YTHDC1 and the cytoplasmic m(6)A reader YTHDF2. Both YTHDC1 and YTHDF2 bind to multiple distinct and overlapping sites on the HIV-1 RNA genome, with YTHDC1 recruitment serving to regulate the alternative splicing of HIV-1 RNAs. Unexpectedly, while YTHDF2 binding to m(6)A residues present on cellular mRNAs resulted in their destabilization as previously reported, YTHDF2 binding to m(6)A sites on HIV-1 transcripts resulted in a marked increase in the stability of these viral RNAs. Thus, YTHDF2 binding can exert diametrically opposite effects on RNA stability, depending on RNA sequence context.