Transcriptome-wide m(6)A methylome analysis uncovered the changes of m(6)A modification in oral pre-malignant cells compared with normal oral epithelial cells

As the most common post-transcriptional RNA modification, m(6)A methylation extensively regulates the structure and function of RNA. The dynamic and reversible modification of m(6)A is coordinated by m(6)A writers and erasers. m(6)A reader proteins recognize m(6)A modification on RNA, mediating different downstream biological functions. mRNA m(6)A modification and its corresponding regulators play an important role in cancers, but its characteristics in the precancerous stage are still unclear. In this study, we used oral precancerous DOK cells as a model to explore the characteristics of transcriptome-wide m(6)A modification and major m(6)A regulator expression in the precancerous stage compared with normal oral epithelial cell HOEC and oral cancer cell SCC-9 through MeRIP-seq and RT-PCR. Compared with HOEC cells, we found 1180 hyper-methylated and 1606 hypo-methylated m(6)A peaks and 354 differentially expressed mRNAs with differential m(6)A peaks in DOK cells. Although the change of m(6)A modification in DOK cells was less than that in SCC-9 cells, mRNAs with differential m(6)A in both cell lines were enriched into many identical GO terms and KEGG pathways. Among the 20 known m(6)A regulatory genes, FTO, ALKBH5, METTL3 and VIRMA were upregulated or downregulated in DOK cells, and the expression levels of 10 genes such as METTL14/16, FTO and IGF2BP2/3 were significantly changed in SCC-9 cells. Our data suggest that precancerous cells showed, to some extent, changes of m(6)A modification. Identifying some key m(6)A targets and corresponding regulators in precancerous stage may provide potential intervention targets for the prevention of cancer development through epigenetic modification in the future.