Fig 2: Identification of drugs with sensitivity associated gene sets enriched with proximal NCOR1 binding using NCI-60 data. (A) Erythroid differentiation in response to Imatinib and Nilotinib. Cell were treated with 500 nM Imatinib or 24 nM Nilotinib for 72 h. Subsequently, cells were stained with benzidine solution. The images were analyzed with CellProfiler to determine the proportion of benzidine-positive cells and K562-shNCOR1 cells were compared to K562-shCTR using t-test. K562-shNCOR1 cells showed significantly reduced erythroid differentiation upon treatment for the both the drugs tested. (B) Volcano plots depicting expression changes upon Imatinib treatment (500 nM, 48 h) in K562-shCTR cells (upper) and K562-shNCOR1 cells (middle). Genes with proximal NCOR1 binding (Nt) are shown in red for DEGs (FDR = 0.05, FC > 1.3). Venn diagram showing comparison of DEGs induced by Imatinib treatment in K562-shCTR and K562-shNCOR1 cells (bottom). (C) Heatmap of Imatinib induced Log2 Fold Change corresponding to all DEGs in both K562-shCTR and K562-NCOR1 cells (n = 2131). Biological replicates are shown, and both sample and genes are clustered using Euclidean distance and complete linkage. Also, the magnitude of absolute expression change induced by Imatinib in each cell line was directly compared.

Fig 3: Recruitment of NCOA1, but not NCOR1, to chromatin is influenced by SUMOylation status of GR. (A) Heat maps showing GR, NCOA1, NCOR1 and SUMO2/3 ChIP-seq profiles from HEK293flpGRwt (wt) and HEK293flpGR3KR (3KR) cells in the presence and absence of Dex. Each heat map represents ±1 kb around the center of the GR peak. C1 represent GRwt preferred, C2 shared, and C3 GR3KR preferred binding sites. Only top 10 000 sites (top 10k) are shown for C2. Binding intensity (tags per bp per site) scale is noted below on a linear scale. All heat maps are normalized to a total of 10 million reads, and further to local tag density. (B–D) Box plots representing normalized log2 tag density of Dex/EtOH for (B) NCOA1 (C) NCOR1 and (D) SUMO2/3 at C1 (blue), C2 (black) and C3 (red) sites. P-values were calculated using unpaired two-sample t-test. All box plots are normalized to total of 10 million reads.

Fig 4: Putative mechanism for altered lung lipid metabolism in Mecp2/Y cells. Schematic of genes in lipid synthesis pathways, highlighting genes with altered expression in Mecp2/Y AE2 cells based on single-cell RNA sequencing. All genes shown have altered gene expression with a P-value <0.05. Arrows indicate direction of metabolic reaction. Genes in red are targets of NCOR1/2-mediated repression. Cytoplasmic genes in blue have decreased expression in Mecp2/Y AE2 cells and are potential targets of SREBPs. Mitochondrial genes in blue have reduced expression in Mecp2/Y AE2 cells and may be altered downstream of other metabolic changes.

Fig 5: Expression analysis in K562-shNCOR1 cells. Volcano plot showing DEGs in K562 shNCOR1 cells compared to K562 shControl cells. Red dots show the genes associated with proximal NCOR1 binding (±1 kb of TSS). Dotted lines show the fold change and P-value cut offs. Genes down-regulated upon NCOR1 knockdown were significantly enriched for the genes associated with the proximal NCOR1 cistrome.