Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise

Regulatory circuitry of a fast-fiber-specific exercise-related TF: PPARD. (A) Example of a regulatory circuit (PPARD-FABP3) in which TF PPARD interacts with a cis-regulatory region upstream of the target gene FABP3 and regulates its expression after exercise. (Left) The normalized chromatin accessibility of the genomic regions around the transcription start site (TSS) of FABP3 in fast fibers pre-exercise (gray) and postexercise (purple). Red arrow indicates the location of the PPARD binding site. (Right) Violin plots showing the expression of FABP3 and PPARD pre-exercise (gray) and postexercise (purple). (B) Estimated TF activity as normalized pseudobulk RNA expression of PPARD in each group, time point, and cell type is depicted as a boxplot with one point per sample. For each group and cell type, both the pre-exercise and postexercise RNA expressions of each sample were normalized by the mean of the pre-exercise samples. (C) Network plot reveals the cell-type-specific target genes (blue) of PPARD (orange) identified by the integrated regulatory circuit analysis. Selected GO terms enriched in the target genes are annotated below. (D,E) Log₂ fold-change (log₂FC) between postexercise and pre-exercise of the target genes (D) and chromatin regions (E) in the fast-fiber-specific PPARD circuitry in each cell type. P-values are calculated using a one-sided Wilcoxon test comparing the log₂FC between fast fibers and other cell types.