Extended Data Fig. 3: nSREBP2 contributes to the formation of cholesterol depletion induced super-enhancer. | Nature Metabolism

Extended Data Fig. 3: nSREBP2 contributes to the formation of cholesterol depletion induced super-enhancer.

From: Nuclear SREBP2 condensates regulate the transcriptional activation of lipogenic genes and cholesterol homeostasis

Extended Data Fig. 3

a, Venn diagram showing the overlapped genes with super-enhancer among HeLa cells treated with FBS, cholesterol-depletion and SREBP target genes from mouse liver microarray. b, Genome browser view of SREBP2 and H3K27Ac ChIP-seq data at the HMGCR, LDLR, SQLE and FASN gene locus in HeLa cells under FBS or cholesterol-depletion condition. c, DNA sequencing results of SREBP2 and SREBP1 knockout HeLa cells. d, Volcano plot showing the up- and down-regulated genes (padj < 0.05, Log2FC > 1 or < -1) from SREBP1 KO HeLa cells with FBS or cholesterol-depletion by RNA-seq. R package DESeq2 calculates two-sided p values by default using the Wald test and performs adjustments for multiple testing. e, Heatmap analysis showing the differential expressed genes of cholesterol synthesis pathway by RNA-seq from WT and SREBP2 KO HeLa cells. f, The top enriched upregulated pathways by GO analysis in Fig. 3d. R package clusterProfiler calculates one-sided p values by hypergeometric test and performs adjustments for multiple testing. g, Motif enrichment from the cholesterol-depletion upregulated genes by RNA-seq using HOMER. A one-sided multiple hypergeometric test for enrichment of motifs in the target sequences compared to the background.

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