(A) De novo motif enrichments around the TSSs of GFEM-associated genes. ATAC-Seq peaks of day 4 after CTX Ly6C^lo repair muscle MFs within 50 kb of TSSs were selected as input. Detected motif matrices, P values, and background are shown. (B) Predicted scores and motif map of 2 distal enhancers (E1, E2) and 1 proximal (P) site around the Gpnmb locus, selected based on ATAC-Seq. Open and closed circles indicate the absence or presence of corresponding TF mRNA, respectively. Motifs of ATF3 and JUN are highlighted. (C) Genome browser view of the Gpnmb locus depicting capture Hi-C (in naive BMDMs), ATAC-Seq (blood monocyte and muscle-infiltrating MFs; normalized scale), and ChIP-Seq (in naive BMDMs and muscle-infiltrating MFs) for indicated TFs, active transcription histone marks (H3K27Ac), and elongating polymerase II (S2P). CTCF and RAD21-defined transcriptional unit boundaries, distal (E1, green; E2, blue) and proximal (P, red) Gpnmb-associated regulatory elements and track scales are indicated. (D) Heatmap of the highest expressed TFs (decile filtered) in the myeloid subtypes of the CTX scRNA-Seq dataset (Figure 2F). Hierarchical clustering and average log-normalized expression values are shown. Atf3 is highlighted. (E) Spatial expression feature plots of top TFs with detected binding in the regulatory elements in the D2.mdx samples. (F) Magnified view of Atf3 spatial expression in representative RIZs in untreated 2-mo D2.mdx muscles. The correlation of observed/expected zone organization is quantified per subspot for each zone and indicates an overlap of Atf3 with zone B. Data (left and middle) have been previously presented in Figure 4A and Figure 7A, respectively, and provide the location and context for the magnified feature plot and expected spatial organization. Scale bars: 500 μm (E, left panel, F). (G) IF region of a lesion in 2-mo D2.mdx GAST muscle. MF subtypes were visualized with CCL2 (red, zone A) and ATF3 (yellow, zone B), and regenerating fibers with eMyHC (green, zone C). Scale bar: 100 μm. (H) Volcano plot showing the DEGs in the Atf3^–/– naive BMDMs (P < 0.01, FDR < 0.01). Number of DEGs and gene labels of GFEM-predicted markers among top DEGs are shown. (I) Atf3 mRNA expression in WT and Atf3^–/– naive BMDMs (n = 3; unpaired t test, P < 0.0001).