Fig. 3: Characterization of the cell-type-specific regulatory landscape in denervated muscle.
From: Reprogramming of cis-regulatory networks during skeletal muscle atrophy in male mice
a Immunofluorescence staining of nuclei and chromatin in normal (left) and denervated (right) GAS muscle, with laminin in red and DAPI in blue. Scale bar: 50 μm. Electron microscopic images are provided for visualization of heterochromatin and nucleoli. b UMAP plot displaying distributions of chromatin accessibility in normal (left) and denervated (right) muscle. c Scatter-box plot illustrating the average number of detected regions in normal and denervated muscles. Data are presented as mean ± SEM (n = 3 mice/group), Significance was evaluated using a two-tailed unpaired t-test (t = 4.337, df = 4). d Fragment coverage plot displaying peak regions over chromosome 1-3 in normal (upper) and denervated (lower) muscle. e Bar plot of annotated the locations of differentially accessible regions (DARs) for each cell type. f Number of DARs between normal and denervated muscle categorized by cell type. g Heatmaps displaying normalized snRNA-seq expression of genes with altered expression linked to DARs between normal and denervated myonuclei. A complete list of these genes is provided in Supplementary data 3. h Fragment coverage tracks illustrating chromatin accessibility and gene expression in normal versus denervated myonuclei. The purple (normal muscle) and red (denervated muscle) lines represent co-accessibility link scores for DARs, deeper in color indicating higher interaction levels. Pink-shaded regions highlight ACRs that overlap with gene promoter areas, while light blue-shaded regions pinpoint distal intergenic areas that show significant co-accessibility with promoter regions. i Dot plot depicting the comparison of Gene Ontology (GO) function enrichment between normal and denervated myonuclei. Dot color corresponds to p-values from the Benjamini-Hochberg-adjusted one-sided hypergeometric test, dot size represents the gene ratio of a GO term. j Heatmaps displaying expression levels of genes linked by co-accessibility to DARs between normal and denervated FAPs. k Fragment coverage tracks depicting chromatin accessibility and gene expression for chosen genes in normal and denervated FAPs. The color schemes align with those described in (h). l Comparison of GO function enrichment between normal and denervated FAPs. The color and size criteria for the dots are described in (i). Source data are provided as a Source data file.
