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Fig. 4 | Genome Medicine

Fig. 4

From: ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

Fig. 4

Enhancer ASXL3 determines the expression of nearby genes. a ASXL3 was knocked down by two different shRNAs. RNA-seq was performed for NCI-H1963 cells transduced with non-targeting shRNA, and two different ASXL3-specific shRNAs, n = 2. b GSEA analysis shows the most enriched gene expression signature in ASXL3-depleted cells. c Real-time PCR was performed to determine the relative gene expression of GADD45A, BCL2, and TCF4 in NCI-H1963 cells transduced with non-targeting shRNA, and two different ASXL3-specific shRNAs, n = 3, two-tailed unpaired Student’s t test. **P < 0.01; *P < 0.05. d Heatmaps generated from ChIP-seq data analysis showing the occupancy of ASXL3, BRD4, H3K4me1, and H3K27Ac at ASXL3 binding sites. All rows are centered at ASXL3 peaks and then further divided into TSS and non-TSS regions. The right panel shows the log2 fold change of nearby gene expression in NCI-H1963 cells transduced with non-targeting shRNA or ASXL3-specific shRNAs, n = 2. e Histone H3 lysine 27 acetylation (H3K27ac) signals from chromatin immunoprecipitation (ChIP) sequencing identifies putative super enhancers (SEs) in NCI-H1963 cells. Hockey-stick plot representing the normalized rank and signals of H3K27Ac. Representative SE-associated genes that are controlled by ASXL3 are labeled. f Representative tracks showing the enhancer binding of ASXL3 and BRD4, which contributes to activation of gene expression

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