BackgroundRNA modifications are important regulators of transcript activity and an increasingly emerging body of data suggests that the epitranscriptome and its associated enzymes are altered in human tumors.MethodsCombining data mining and conventional experimental procedures,NSUN7methylation and expression status was assessed in liver cancer cell lines and primary tumors. Loss-of-function and transfection-mediated recovery experiments coupled with RNA bisulfite sequencing and proteomics determined the activity of NSUN7 in downstream targets and drug sensitivity.ResultsIn this study, the initial screening for genetic and epigenetic defects of 5-methylcytosine RNA methyltransferases in transformed cell lines, identified that the NOL1/NOP2/Sun domain family member 7 (NSUN7) undergoes promoter CpG island hypermethylation-associated with transcriptional silencing in a cancer-specific manner.NSUN7epigenetic inactivation was common in liver malignant cells and we coupled bisulfite conversion of cellular RNA with next-generation sequencing (bsRNA-seq) to find the RNA targets of this poorly characterized putative RNA methyltransferase. Using knock-out and restoration-of-function models, we observed that the mRNA of the coiled-coil domain containing 9B (CCDC9B) gene required NSUN7-mediated methylation for transcript stability. Most importantly, proteomic analyses determined that CCDC9B loss impaired protein levels of its partner, the MYC-regulator Influenza Virus NS1A Binding Protein (IVNS1ABP), creating sensitivity to bromodomain inhibitors in liver cancer cells exhibitingNSUN7epigenetic silencing. The DNA methylation-associated loss ofNSUN7was also observed in primary liver tumors where it was associated with poor overall survival. Interestingly,NSUN7unmethylated status was enriched in the immune active subclass of liver tumors.ConclusionThe 5-methylcytosine RNA methyltransferaseNSUN7undergoes epigenetic inactivation in liver cancer that prevents correct mRNA methylation. Furthermore,NSUN7DNA methylation-associated silencing is associated with clinical outcome and distinct therapeutic vulnerability.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12943-023-01785-z.