Systematic identification of tissue-conserved m6A sites reveals a stable epitranscriptomic regulatory layer controlling essential genes

Abstract

Chemical modifications to RNA are fundamental regulators of cellular identity and function. Among these, N6-methyladenosine (m6A) is the most abundant mRNA modification in mammalian cell, governing major post-transcriptional processes. While conditional m6A dynamics are well studied, the extent and function of condition-independent, tissue-conserved (TC) m6A 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. RBM15/B are identified as candidate mediators of TC m6A deposition, and YTHDF1-3 and UPF1 are preferentially enriched at TC sites, supporting their role for m6A-linked mRNA decay. TC m6A 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 m6A genes are disproportionately differentially expressed, alongside with altered RBM15/B expression, suggesting that disruption of this stable m6A layer may contribute to transcriptional changes in cancer.