Epitranscriptomics m6A analyses reveal distinct m6A marks under tumor necrosis factor α (TNF‐α)‐induced apoptotic conditions in HeLa cells

Tumor necrosis factor‐α (TNF‐α) is a ligand that induces both intrinsic and extrinsic apoptotic pathways in HeLa cells by modulating complex gene regulatory mechanisms. However, the full spectrum of TNF‐α‐modulated epitranscriptomic m6A marks is unknown. We employed a genomewide approach to examine the extent of m6A RNA modifications under TNF‐α‐modulated apoptotic conditions in HeLa cells. miCLIP‐seq analyses revealed a plethora of m6A marks on 632 target mRNAs with an enrichment on 99 mRNAs associated with apoptosis. Interestingly, the m6A RNA modification patterns were quite different under cisplatin‐ and TNF‐α‐mediated apoptotic conditions. We then examined the abundance and translational efficiencies of several mRNAs under METTL3 knockdown and/or TNF‐α treatment conditions. Our analyses showed changes in the translational efficiency of TP53INP1 mRNA based on the polysome profile analyses. Additionally, TP53INP1 protein amount was modulated by METTL3 knockdown upon TNF‐α treatment but not CP treatment, suggesting the existence of a pathway‐specific METTL3‐TP53INP1 axis. Congruently, METLL3 knockdown sensitized HeLa cells to TNF‐α‐mediated apoptosis, which was also validated in a zebrafish larval xenograft model. These results suggest that apoptotic pathway‐specific m6A methylation marks exist in cells and TNF‐α‐METTL3‐TP53INP1 axis modulates TNF‐α‐mediated apoptosis in HeLa cells. TNF‐α‐METTL3‐TP53INP1 is a new axis that appears to modulate the extrinsic pathway of apoptosis in HeLa cells. Five adenosine residues which are methylated under control conditions. There is a nice correlation between the enhanced translation of TP53INP1 transcript and its reduced m6A RNA methylation under tumor necrosis factor‐α treatment or METTL3 knockdown conditions, which leads to enhanced apoptosis.