Additional file 3: of BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells

Figure S1. Example of a super-enhancer shared by BRCA1+/+ and BRCA1mut/+ HMECs. Track view of H3K27ac ChIP-seq density profile centered at a BRCA1+/+ and BRCA1mut/+ HMECs-shared super-enhancer. Each track represents one biological sample with BRCA1+/+ colored blue and BRCA1mut/+ colored red. Locations of the super-enhancer are shaded and marked by a black bar, and TSS was marked by an arrow. Figure S2. Quantification of H3K27ac in BRCA1185delAG/+ MCF10A cells. Quantification of H3K27ac Western blot normalized by H3. Bar graph depicts the average of three independent experiments with WT MCF10A and BRCA1185delAG/+ MCF10A. Error bars represent s.e.m. n.s.: not significant by two-tailed t test. Figure S3. BRCA1 and CTCF ChIP-seq tracks. (A) Track view of published BRCA1 ChIP-seq [38, 39] and CTCF ChIP-seq [38] density profile centered on SOD2 super-enhancer. Two CTCF peaks were marked. (B) Track view of existing BRCA1 ChIP-seq [38, 39] density profile centered on TNFAIP3 super-enhancer. Locations of the super-enhancers are shaded and marked by solid bars, and TSSs are marked by arrows. Locations of the ChIP primers are marked in red. Figure S4. BRD4 level is not affected in BRCA1185delAG/+ MCF10A clones. (A) Western blot of BRD4 in WT and BRCA1185delAG/+ MCF10A clones. α-Tubulin was used as the loading control. (B) Quantification of BRD4 western blot normalized by α-Tubulin. Bar graph depicts the average of three independent experiments with WT MCF10A and BRCA1185delAG/+ MCF10A. Figure S5. Lower BRD4-H3K27ac co-occupancy in BRCA1185delAG/+ MCF10A clones. (A) Relative ChIP-re-ChIP signal at SOD2 super-enhancer. The graph is an average of two independent experiments. (B) Relative ChIP-re-ChIP signal at TNFAIP3 super-enhancer. The graph is an average of two independent experiments. *P < 0.05 by two-tailed t test. Error bars represent s.e.m. Figure S6. CTCF level is not affected in BRCA1185delAG/+ MCF10A clones. (A) Western blot of CTCF in WT and BRCA1185delAG/+ MCF10A clones. α-Tubulin was used as loading control. (B) Quantification of CTCF western blot normalized by α-Tubulin. Bar graph depicts the average of three independent experiments. Error bars represent s.e.m. n.s.: not significant by two-tailed t-test. Figure S7. Lower WT BRCA1 expression in BRCA1185delAG/+ MCF10A clones. Western blot of BRCA1 in WT and BRCA1185delAG/+ MCF10A clones. α-Tubulin was used as the loading control. (PPTX 170 kb)