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A) Genomic Locus Overlap Enrichment Analysis (LOLA) of differentially accessible regions (DARs) between day 13 and day 11, stratified according to the four clusters defined in A) (open promoter, n = 477 DARs; open distal, n = 368 DARs; closed promoter, n = 309 DARs; closed distal, n = 1,008 DARs). Enrichment was performed against the database of transcriptional regulators peaks from ReMap2022. Statistical significance was assessed using Fisher’s exact test implemented in LOLA (FDR-adjusted p < 0.05). The x-axis represents the odds ratio, and adjusted FDR values are indicated in the labels (ns, grey; FDR < 0.05, light blue; FDR < 0.005, blue; FDR < 0,0005 dark blue). The background universe corresponds to all accessible regions detected in the ATAC-Seq dataset. B) Functional enrichment analysis of the nearest associated genes to the defined DARs using ChEA gene sets. , Enrichment was assessed using a one-sided hypergeometric test with false discovery rate correction (Benjamini–Hochberg). The x-axis shows the number of enriched genes, and adjusted P values are indicated in the labels. The background gene universe corresponds to all genes associated with peak detected in the ATAC-seq dataset. C) Heatmap of differentially expressed genes (DEGs) induced by BAF inhibition, identified by comparing BAF inhibitor–treated samples <t>(BRM/BRG1</t> ATP Inhibitor-1 - <t>BRM014;</t> 0.016, 0.08, and 0.4 µM; pink gradient from light to dark) to untreated controls. The inhibitor was applied at day 12 and RNA was collected at day 13 (DESeq2 with apeglm LFC shrinkage; adjusted p < 0.05; |fold change| > 1.5). Expression values are scaled by row (turquoise to yellow).
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A) Genomic Locus Overlap Enrichment Analysis (LOLA) of differentially accessible regions (DARs) between day 13 and day 11, stratified according to the four clusters defined in A) (open promoter, n = 477 DARs; open distal, n = 368 DARs; closed promoter, n = 309 DARs; closed distal, n = 1,008 DARs). Enrichment was performed against the database of transcriptional regulators peaks from ReMap2022. Statistical significance was assessed using Fisher’s exact test implemented in LOLA (FDR-adjusted p < 0.05). The x-axis represents the odds ratio, and adjusted FDR values are indicated in the labels (ns, grey; FDR < 0.05, light blue; FDR < 0.005, blue; FDR < 0,0005 dark blue). The background universe corresponds to all accessible regions detected in the ATAC-Seq dataset. B) Functional enrichment analysis of the nearest associated genes to the defined DARs using ChEA gene sets. , Enrichment was assessed using a one-sided hypergeometric test with false discovery rate correction (Benjamini–Hochberg). The x-axis shows the number of enriched genes, and adjusted P values are indicated in the labels. The background gene universe corresponds to all genes associated with peak detected in the ATAC-seq dataset. C) Heatmap of differentially expressed genes (DEGs) induced by BAF inhibition, identified by comparing BAF inhibitor–treated samples (BRM/BRG1 ATP Inhibitor-1 - BRM014; 0.016, 0.08, and 0.4 µM; pink gradient from light to dark) to untreated controls. The inhibitor was applied at day 12 and RNA was collected at day 13 (DESeq2 with apeglm LFC shrinkage; adjusted p < 0.05; |fold change| > 1.5). Expression values are scaled by row (turquoise to yellow).

Journal: bioRxiv

Article Title: A Conserved Chromatin-Driven Checkpoint Defines Late Macrophage Maturation Independent of Tissue Specialization

doi: 10.64898/2026.07.01.735834

Figure Lengend Snippet: A) Genomic Locus Overlap Enrichment Analysis (LOLA) of differentially accessible regions (DARs) between day 13 and day 11, stratified according to the four clusters defined in A) (open promoter, n = 477 DARs; open distal, n = 368 DARs; closed promoter, n = 309 DARs; closed distal, n = 1,008 DARs). Enrichment was performed against the database of transcriptional regulators peaks from ReMap2022. Statistical significance was assessed using Fisher’s exact test implemented in LOLA (FDR-adjusted p < 0.05). The x-axis represents the odds ratio, and adjusted FDR values are indicated in the labels (ns, grey; FDR < 0.05, light blue; FDR < 0.005, blue; FDR < 0,0005 dark blue). The background universe corresponds to all accessible regions detected in the ATAC-Seq dataset. B) Functional enrichment analysis of the nearest associated genes to the defined DARs using ChEA gene sets. , Enrichment was assessed using a one-sided hypergeometric test with false discovery rate correction (Benjamini–Hochberg). The x-axis shows the number of enriched genes, and adjusted P values are indicated in the labels. The background gene universe corresponds to all genes associated with peak detected in the ATAC-seq dataset. C) Heatmap of differentially expressed genes (DEGs) induced by BAF inhibition, identified by comparing BAF inhibitor–treated samples (BRM/BRG1 ATP Inhibitor-1 - BRM014; 0.016, 0.08, and 0.4 µM; pink gradient from light to dark) to untreated controls. The inhibitor was applied at day 12 and RNA was collected at day 13 (DESeq2 with apeglm LFC shrinkage; adjusted p < 0.05; |fold change| > 1.5). Expression values are scaled by row (turquoise to yellow).

Article Snippet: On day 12, cells were treated for 24 h with the BRM/BRG1 ATPase (SWI/SNF) inhibitor BRM014 (MedChemExpress, cat. no. HY-119374) at final concentrations of 400, 80, or 16 nM, with PBS-treated wells included as controls.

Techniques: Functional Assay, Inhibition, Expressing