Fig. 1: Transcriptome dynamics and genome-wide analysis of CREs in SOL and EDL.

a Isolated EDL and SOL muscles. b Representative immunofluorescent staining of slow-twitch MyHC I (red) and fast-twitch MyHC IIb (green) in SOL and EDL sections. Magnification: ×20, Bar = 200 μm. c Heatmap of muscle fiber-type marker gene expression. d Classification and annotation of chromatin states, with each row representing a chromatin state and each column denoting histone marks, chromatin accessibility, genomic annotation, and gene expression levels. TssAFlank1 (n = 56, median = 1.076648): high H3K4me3 and ATAC-seq signal; TssAFlank2 (n = 214, median = 1.129079): high H3K4me3 but weak ATAC-seq signal. EnhA1 (n = 55, median = 1.476194): high H3K27ac and ATAC-seq signal; EnhA2 (n = 161, median = 1.460204): weak H3K27ac and ATAC-seq signal. RepPC (n = 65, median = 0.5147669): high H3K27me3 signal. Quiescent (n = 192, median = 0.6704646): lack epigenetics signal. e Tissue specificity of identified CREs. f Alluvial diagram depicting changes in promoter chromatin states of DEGs. g Expression changes of DEGs with switched chromatin states. Boxes represent the interquartile range with the median as a horizontal line; whiskers extend to the 5th and 95th percentiles. Significance was tested using a two-sided Wilcoxon test. h Functional enrichment analysis of tissue-specific enhancers using GREAT. Significance was tested using binomial test. i ATAC-seq tracks, chromatin states, and histone modifications at SLN and UQCR10 loci and their associated enhancers in SOL and EDL.