m6A and YTHDF1, YTHDF2, YTHDF3 mapping of the HIV-1 RNA pool with PAR-CLIP and pA-m6A-seq. Homo sapiens

To replicate in the host, HIV-1 must produce RNA and protein, and this depends cellular factors that also control gene expression. Recently, it has been shown that novel components of this machinery post-transcriptionally modify mRNAs with direct consequences for their structure and stability. The most common among these modifications is the addition of a methyl group to the N6 position of adenosine, termed m6A methylation. Here we are interested the interface of HIV-1 with this posttranscriptional mRNA modification pathway. We show that viral transcripts harbor a number of discrete methylation sites and are bound at those sites by these YTHDF proteins. These sites are conserved among distinct HIV-1 isolates and are observed during viral replication in numerous cell types. With reporter assays we also show that these sites stabilize mRNAs when compared to similar sequences mutated to be incapable of methylation. We further show that overexpression of these reader proteins boosts viral protein expression. Overall design: In this GEO submission we include the PAR-CLIP data sets for numerous HIV-1 isolates in 293T cells, and pA-m6A-seq in CEM-SS cells