m(6)A-mRNA Methylation Regulates Gene Expression and Programmable m(6)A Modification of Cellular RNAs With CRISPR-Cas13b in Renal Cell Carcinoma

Background: N(6)-methyladenosine (m(6)A) is the most extensive messenger RNA modification. Despite recent advances in the biological roles of m(6)A, its role in the development and progression of renal cell carcinoma (RCC) remains unclear. Methods: In this study, we gained the transcriptome-wide m(6)A profile and gene expression pattern in RCC and paired adjacent peritumoral tissues by meRIP-seq and RNA-seq. m(6)A modifications of mRNAs were validated by meRIP-qPCR in tissues, and targeted methylation or demethylation was validated by using a CRISPR-Cas13b-based tool in RCC cell lines. Results: Our findings showed that there were 13,805 m(6)A peaks among 5,568 coding gene transcripts (mRNAs) in adjacent tissues and 24,730 m(6)A peaks among 6,866 mRNAs in tumor tissues. Furthermore, m(6)A modification sites were usually located in the coding sequences (CDS), and some near the start and stop codons. Gene Ontology analysis revealed that coding genes had differential N(6)-methyladenosine sites and were enriched in kidney development and cancer-related signaling pathways. We also found that different levels of m(6)A modifications could regulate gene expression. Conclusion: In summary, our results provided evidence for studying the potential function of RNA m(6)A modification and m(6)A-mediated gene expression regulation in human RCC.