HIV reprograms host m6Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1

Abstract N 6 ,2′- O -dimethyladenosine (m 6 Am) is an abundant RNA modification located adjacent to the 5′-end of the mRNA 7-methylguanosine (m 7 G) cap structure. m 6 A methylation on 2′- O -methylated A at the 5′-ends of mRNAs is catalyzed by the methyltransferase Phosphorylated CTD Interacting Factor 1 (PCIF1). The role of m 6 Am and the function of PCIF1 in regulating host–pathogens interactions are unknown. Here, we investigate the dynamics and reprogramming of the host m 6 Am RNA methylome during HIV infection. We show that HIV infection induces a dramatic decrease in m 6 Am of cellular mRNAs. By using PCIF1 depleted T cells, we identify 2237 m 6 Am genes and 854 are affected by HIV infection. Strikingly, we find that PCIF1 methyltransferase function restricts HIV replication. Further mechanism studies show that HIV viral protein R (Vpr) interacts with PCIF1 and induces PCIF1 ubiquitination and degradation. Among the m 6 Am genes, we find that PCIF1 inhibits HIV infection by enhancing a transcription factor ETS1 (ETS Proto-Oncogene 1, transcription factor) stability that binds HIV promoter to regulate viral transcription. Altogether, our study discovers the role of PCIF1 in HIV–host interactions, identifies m 6 Am modified genes in T cells which are affected by viral infection, and reveals how HIV regulates host RNA epitranscriptomics through PCIF1 degradation.