Fibrillarin-mediated 2'-O-methylation serves as a translation brake on uncapped enterovirus RNA

To systematically investigate the landscape and functional significance of internal Nm modifications on enterovirus RNAs, a sensitive sequencing method termed RACE-Nm was established, in combination with the machine learning–based predictor NanoNm, to map Nm sites on low-abundance RNAs at single-nucleotide resolution.

A conserved Nm site was identified at nucleotide 307C within the viral internal ribosome entry site (IRES), which was catalyzed by the methyltransferase FBL. The 2′-O-methylation at 307C caused steric hindrance that disrupted PCBP2 recruitment to the IRES and repressed cap-independent translation. Consequently, FBL-mediated suppression of IRES activity limited the production of the viral RNA polymerase 3D, which in turn prevented the upregulation of a set of pro-viral host genes, including FOSL1, ITGB3, KCNQ4, and TFPI2.