N(6)-methyladenosine modification of RNA is regulated by senataxin and E6 to control HPV replication

The levels of N6-methyladenosine (m6A)-modified RNAs are reduced within cells with high-risk human papillomaviruses (HPVs) in comparison to normal cells. These reduced m6A levels stabilize RNA:DNA hybrids (R-loops), whose regulation is critical for viral replication. HPV E6 induces the degradation of the m6A methyltransferases, Mettl3 and Mettl14, in an E6AP-dependent manner to reduce m6A levels, while the RNA helicase senataxin (SETX) counteracts this by activating the expression of m6A regulators. Maintenance of the residual m6A levels in undifferentiated cells is also critical for viral replication. A subset of early viral transcripts is m6A modified, and the inhibition of Mettl3 impairs viral gene expression. Upon differentiation, the levels of SETX and m6A are increased by over 8-fold, which is necessary for the productive replication of HPVs. These studies identify a role for SETX and E6 in regulating m6A deposition to control HPV pathogenesis in a differentiation-dependent manner.