Dynamic tRNA modification landscapes reveal METTL1 in fibroblasts as a central regulator of aging

RNA modifications have emerged as crucial regulators of cellular processes linked to aging. However, the dynamic changes in global RNA modification patterns during aging and their functional implications remain underexplored. Here, we comprehensively deciphered the RNA modification landscapes of total RNA, poly(A)-enriched mRNA, and tRNA-enriched fragments across six tissues in both young and aged mice, as well as in multiple cellular senescence models. Aged tissues exhibit overall decline of RNA modification abundance in tRNA, rather than in total RNA or mRNA, when compared to young tissues. Correspondingly, the expression of tRNA methyltransferases, METTL1 and TRMT1, also declines with aging and senescence. Modulation of these methyltransferases affects cellular senescence phenotypes; specifically, Mettl1 depletion results in accelerated aging in mice. Mechanistically, fibroblasts are identified as the primary cell type responsible for the aging traits induced by Mettl1 deficiency in mice. Reduced m⁷G modification in fibroblasts leads to a decrease in the abundance of m⁷G-modified tRNAs, which in turn impairs translation efficiency and protein synthesis, and contributes to an accumulation of tRNA-derived small RNAs (tsRNAs). Remarkably, these alterations affected the translation of genes involved in senescence and aging pathways. Our study provides a comprehensive landscape of tRNA modifications during aging and demonstrates that decreased activity of METTL1 in fibroblasts drives aging. Thus, modulation of tRNA modifications may be a promising strategy for improving healthy aging and alleviating age-associated disorders.