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. 2022 Nov 29;21(3):274–289. doi: 10.1158/1541-7786.MCR-22-0772

Figure 5.

Figure 5. MUC1-C/PBRM1/IRF1 complexes induce chromatin accessibility and expression of the RIG-I, MDA5, and ISG15 genes. A, Candidate pathway enrichment plot for the IFNA response in BT-549 cells silenced for MUC1-C, IRF1, and PBRM1. B and C, Genome browser snapshots of ATAC-seq data from the RIG-I (B) and MDA5 (C) PLSs in BT-549/tet-MUC1shRNA cells treated with vehicle or DOX for 7 days (left). Chromatin was analyzed for accessibility by nuclease digestion (right). The results are expressed as the percentage of undigested chromatin (mean±SD and individual values). D and E, Schema of the RIG-I (D) and MDA5 (E) genes with localization of a PLS upstream to the TSS. Soluble chromatin from BT-549/tet-MUC1shRNA cells treated with vehicle or DOX for 7 days was precipitated with a control IgG, anti–MUC1-C, anti-IRF1 and anti-PBRM1. The DNA samples were amplified by qPCR with primers for the RIG-I (D) and MDA5 (E) PLS regions. The results (mean±SD and individual values) are expressed as relative fold enrichment as compared with that obtained with IgG (assigned a value of 1). F, Chromatin from BT-549/CshRNA and BT-549/PBRM1shRNA cells was analyzed for accessibility of the RIG-I and MDA5 PLS regions by nuclease digestion. The results are expressed as the percentage of undigested chromatin (mean±SD and individual values). G, Genome browser snapshots of ATAC-seq data from the ISG15 PLS in BT-549/tet-MUC1shRNA cells treated with vehicle or DOX for 7 days (left). Chromatin was analyzed for accessibility by nuclease digestion (right). The results are expressed as the percentage of undigested chromatin (mean±SD and individual values). H, Schema of the ISG15 gene with localization of a PLS upstream to the TSS. Soluble chromatin from BT-549/tet-MUC1shRNA cells treated with vehicle or DOX for 7 days was precipitated with a control IgG, anti-MUC1-C, anti-IRF1, and anti-PBRM1. The DNA samples were amplified by qPCR with primers for the ISG15 PLS region. The results (mean±SD and individual values) are expressed as relative fold enrichment as compared with that obtained with IgG (assigned a value of 1). I, Chromatin from BT-549/CshRNA and BT-549/PBRM1shRNA cells was analyzed for accessibility of the ISG15 PLS region by nuclease digestion. The results are expressed as the percentage of undigested chromatin (mean±SD and individual values).

MUC1-C/PBRM1/IRF1 complexes induce chromatin accessibility and expression of the RIG-I, MDA5, and ISG15 genes. A, Candidate pathway enrichment plot for the IFNA response in BT-549 cells silenced for MUC1-C, IRF1, and PBRM1. B and C, Genome browser snapshots of ATAC-seq data from the RIG-I (B) and MDA5 (C) PLSs in BT-549/tet-MUC1shRNA cells treated with vehicle or DOX for 7 days (left). Chromatin was analyzed for accessibility by nuclease digestion (right). The results are expressed as the percentage of undigested chromatin (mean ± SD and individual values). D and E, Schema of the RIG-I (D) and MDA5 (E) genes with localization of a PLS upstream to the TSS. Soluble chromatin from BT-549/tet-MUC1shRNA cells treated with vehicle or DOX for 7 days was precipitated with a control IgG, anti–MUC1-C, anti-IRF1 and anti-PBRM1. The DNA samples were amplified by qPCR with primers for the RIG-I (D) and MDA5 (E) PLS regions. The results (mean ± SD and individual values) are expressed as relative fold enrichment as compared with that obtained with IgG (assigned a value of 1). F, Chromatin from BT-549/CshRNA and BT-549/PBRM1shRNA cells was analyzed for accessibility of the RIG-I and MDA5 PLS regions by nuclease digestion. The results are expressed as the percentage of undigested chromatin (mean ± SD and individual values). G, Genome browser snapshots of ATAC-seq data from the ISG15 PLS in BT-549/tet-MUC1shRNA cells treated with vehicle or DOX for 7 days (left). Chromatin was analyzed for accessibility by nuclease digestion (right). The results are expressed as the percentage of undigested chromatin (mean ± SD and individual values). H, Schema of the ISG15 gene with localization of a PLS upstream to the TSS. Soluble chromatin from BT-549/tet-MUC1shRNA cells treated with vehicle or DOX for 7 days was precipitated with a control IgG, anti-MUC1-C, anti-IRF1, and anti-PBRM1. The DNA samples were amplified by qPCR with primers for the ISG15 PLS region. The results (mean ± SD and individual values) are expressed as relative fold enrichment as compared with that obtained with IgG (assigned a value of 1). I, Chromatin from BT-549/CshRNA and BT-549/PBRM1shRNA cells was analyzed for accessibility of the ISG15 PLS region by nuclease digestion. The results are expressed as the percentage of undigested chromatin (mean ± SD and individual values). *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.