Alterations of the m6A Methylation Induced by TGF-β2 in ARPE-19 Cells

Abstract

Background: N6-methyladenosine (m6A) participates in diverse physiological processes and contributes to many pathological conditions. Epithelial-mesenchymal transition (EMT) of retinal pigmental epithelial (RPE) cells plays an essential role in retinal-related diseases, and transforming growth factor β2 (TGF-β2) is known to induce EMT in vitro. However, the effect of TGF-β2 on m6A methylation in RPE cells is not yet known. Methods: RNA-seq and MeRIP-seq were performed to analyze changes at the mRNA and m6A levels after TGF-β2 treatment of human ARPE-19 cells. mRNA levels and total m6A levels were subsequently validated. Results: Sequencing revealed 929 differentially expressed genes and 7328 differentially methylated genes after TGF-β2 treatment. Conjoint analysis identified 290 genes related to microtubule cytoskeleton, focal adhesion, ECM-receptor interaction, cell division, cell cycle, AGE-RAGE, PI3K-Akt and cGMP-PKG pathways. Further analysis revealed that 12 EMT-related genes were altered at the mRNA and m6A levels after TGF-β2 treatment (CALD1, CDH2, FN1, MMP2, SPARC, KRT7, CLDN3, ELF3, FGF1, LOXL2, SHROOM3 and TGFBI). Moreover, the total m6A level was also reduced. Conclusions: This study revealed the transcriptional profiling of m6A modification induced by TGF-β2 in RPE cells. Novel connections were discovered between m6A modification and TGF-β2-induced EMT, suggesting that m6A may play crucial roles in the EMT process.

Keywords

• m6a methylation
• rpe cells
• emt
• tgf-β2
• transcriptomics
• merip-seq