Fig. 3. Matr3 depletion alters chromatin accessibility and MyoD binding, which foreshadow later gene expression changes.

a Heatmap showing differential chromatin accessibility (ATAC-seq) at 4 h., 8 h. post Matr3 depletion and steady state (Matr3 KO). Bar chart: percentage of peak increased and decreased per time point. b Same panels with (a) for MyoD binding (CUT&RUN). Gains trended down over time while losses increased. c Genes mapped by differentially chromatin accessible peaks per time point (4 h., 8 h., steady), illustrating the magnitude and number of changes. Accessibility was primarily lost at steady state. d Genes mapped by differential MyoD binding. Particularly striking were MyoD binding gains at 4 h. and loss at steady state. e GO biological process enrichment on differentially ATAC-seq mapped genes (4 h.). f GO enrichment on differential MyoD bound genes (4 h.). In (e, f), hypergeometric test, two-sided were used and Padj values are shown. Adjusted for multiple comparisons by Benjamini and Hochberg (BH) method. g Overlap of differential ATAC and MyoD bound regions (4 h.). P: P value. Hypergeometric test (one-sided) with multiple comparisons by BH method. M: number of co-bound peaks. Number in circle: # of differential peaks. h, i Early differentially accessible and MyoD bound genes elicited expression changes later in development (days 4 and 6). Genes were selected from heatmap in (c, d) as having MyoD 4 h. binding gain or ATAC 4 h. gain/loss. Expression changes (measured by ∆=KO-WT) were followed during development. Expression changes were not significant at day 0 (steady state, both up and down p > 0.1), but evident at days 4, and 6 (both up and down p < 0.00016). Upregulated genes in Matr3 downregulated genes exhibited positive ∆ (h), downregulated genes in Matr3KO show negative ∆ (i). Error bars and bands represent 95% confidence interval of mean. Paired t test, one-sided was used. No multiple comparison is made. Source data are provided as a Source Data file.