Multi-omics atlas of chronic exercise.

Exercise reduces all-cause mortality, yet its molecular effects across organs, sexes, and circadian phases remain incompletely understood. We subjected mice to 8 weeks of voluntary wheel running and collected 22 tissues and plasma during active and inactive phases for bulk RNA sequencing, metabolomics, proteomics, and single-nucleus RNA and methylation sequencing. Exercise induced canonical fiber-type switching and widespread, tissue-specific remodeling, with the largest transcriptomic changes in skeletal muscle. Except for the hypothalamus, kidney, and lung, most tissues changed more during the active phase. Females showed broader transcriptional responses, with distinct downregulation. Pairing single-nucleus methylomes with transcriptomes resolved the cell types driving exercise-induced epigenetic remodeling-changes undetectable by bulk studies. These included coordinated gene-body demethylation and transcription that tracked with fiber-type switching in specific myonuclei. Cell-type-resolved methylation, including partially methylated domains characterized in muscle, revealed a strong, sex-biased epigenetic response to training. Machine learning identified conserved exercise signatures across mammalian species.