Systematic identification of tissue-conserved m ⁶ A sites reveals a stable epitranscriptomic regulatory layer controlling essential genes

Chemical modifications to RNA are fundamental regulators of cellular identity and function. Among these, N6-methyladenosine (m ⁶ A) is the most abundant mRNA modification in mammalian cell, governing major post-transcriptional processes. While conditional m ⁶ A dynamics are well studied, the extent and function of condition-independent, tissue-conserved (TC) m ⁶ A in humans remain unclear. Here we show that 5,945 TC sites are consistently methylated across 24 human tissues. These sites are enriched near stop codons, evolutionarily conserved, and characterized by distinct sequence signatures. <i>RBM15/B</i> are identified as candidate mediators of TC m ⁶ A deposition, and <i>YTHDF1-3</i> and <i>UPF1</i> are preferentially enriched at TC sites, supporting their role for m ⁶ A-linked mRNA decay. TC m ⁶ A sites mark 1,386 genes essential for core cellular processes like autophagy and homeostasis, showing stable expression and evolutionary constraint. Pan-cancer analysis reveals that TC m ⁶ A genes are disproportionately differentially expressed, alongside with altered <i>RBM15/B</i> expression, suggesting that disruption of this stable m ⁶ A layer may contribute to transcriptional changes in cancer.