YTHDC1 regulates distinct post-integration steps of HIV-1 replication and is important for viral infectivity

The recent discovery of the role of m⁶A methylation in the regulation of HIV-1 replication unveiled a novel layer of regulation for HIV gene expression. This epitranscriptomic modification of HIV-1 RNAs is under the dynamic control of specific writers and erasers. In addition, cytoplasmic readers of the m⁶A mark are recruited to the modified viral RNAs and regulate HIV-1 replication. Yet, little is known about the effects of m⁶A writers and readers on the biogenesis of HIV-1 RNAs.

We showed that the METTL3/14 m⁶A methyltransferase complex and the m⁶A YTHDF2 cytoplasmic writer down regulates the abundance of HIV-1 RNAs in infected cells. We also identified the m⁶A nuclear writer YTHDC1 as a novel regulator of HIV-1 transcripts. In HIV-1 producer cells, we showed that knocking down YTHDC1 increases the levels of unspliced and incompletely spliced HIV-1 RNAs, while levels of multiply spliced transcripts remained unaffected. In addition, we observed that depletion of YTHDC1 has no effect on the nuclear cytoplasmic distribution of viral transcripts. YTHDC1 binds specifically to HIV-1 transcripts in a METTL3-dependent manner. Knocking down YTHDC1 reduces the expression of Env and Vpu viral proteins in producer cells and leads to the incorporation of unprocessed Env gp160 in virus particles, resulting in the decrease of their infectivity.

Our findings indicate that, by controlling HIV-1 RNA biogenesis and protein expression, the m⁶A nuclear reader YTHDC1 is required for efficient production of infectious viral particles.