Reprogramming of m 6 A epitranscriptome is crucial for shaping of transcriptome and proteome in response to hypoxia.

Hypoxia causes a series of responses supporting cells to survive in harsh environments. Substantial post-transcriptional and translational regulation during hypoxia has been observed. However, detailed regulatory mechanism in response to hypoxia is still far from complete. RNA m ⁶ A modification has been proven to govern the life cycle of RNAs. Here, we reported that total m ⁶ A level of mRNAs was decreased during hypoxia, which might be mediated by the induction of m ⁶ A eraser, ALKBH5. Meanwhile, expression levels of most YTH family members of m ⁶ A readers were systematically down-regulated. Transcriptome-wide analysis of m ⁶ A revealed a drastic reprogramming of m ⁶ A epitranscriptome during cellular hypoxia. Integration of m ⁶ A epitranscriptome with either RNA-seq based transcriptome analysis or mass spectrometry (LC-MS/MS) based proteome analysis of cells upon hypoxic stress revealed that reprogramming of m ⁶ A epitranscriptome reshaped the transcriptome and proteome, thereby supporting efficient generation of energy for adaption to hypoxia. Moreover, ATP production was blocked when silencing an m ⁶ A eraser, ALKBH5, under hypoxic condition, demonstrating that m ⁶ A pathway is an important regulator during hypoxic response. Collectively, our studies indicate that crosstalk between m ⁶ A and HIF1 pathway is essential for cellular response to hypoxia, providing insights into the underlying molecular mechanisms during hypoxia.