Fig. 5: CUT&RUN analyses of BMI1, RING1B, H2A119ub, and H3K27me3 in iSRE and SRE demonstrate coordinated associations of BMI1 and RING1B on chromatin with variable patterns of histone modifications.
From: BMI1 regulates human erythroid self-renewal through both gene repression and gene activation
See Supplementary Fig. 5A for samples used in CUT& RUN. A shRNA knockdown of RING1B leads to rapid collapse of iSRE cultures. p-value was calculated based on two-way ANOVA of all RING1B shRNA vs Luciferase. 2 independent iSRE cultures from 1 donor, mean ± range, expansion day 30. B Heatmaps of BMI1 enrichment in untransduced (UT) SREs and iSREs over union peaks (±2 kb). The color scale represents the RPKM of each sample using merged replicates. Ranked based on mean RPKMs. C Volcano plot showing differential occupancy of BMI1 in iSRE versus untransduced SREs. Significantly increased and decreased peaks are shown in red and blue, respectively, with FDR < 0.05. D Heatmaps of BMI1 occupancy, RING1B occupancy, H2A119ub, and H3K27me3 over BMI1 differentially increased (top) and decreased (bottom) peaks in untransduced SREs and in iSREs. The color scale represents RPKM of each sample using merged replicates. Ranking was sorted based on BMI1 binding in iSREs. Blue line- increased BMI1 peaks. Orange line- decreased BMI1 peaks. E Heatmaps of BMI1, RING1B, H2A119ub, and H3K27me3 over 2 clusters of BMI1 differentially increased peaks (kmeans=2, clustering based on H3K27me3 in iSREs) in untransduced SREs and in iSREs. The color scale represents RPKM of each sample using merged replicates. Ranking was based on BMI1 binding in iSREs. Blue line- Cluster 1. Orange line- Cluster 2. F Table of selected published gene sets that contain significant overlap with CUT&RUN gene sets (Enrichr). See Supplementary Data 1 for details.
