Extended Data Fig. 6: Identification and characterization of critical target genes of H3P16oh in breast cancer cells.

a, Venn diagram showing genes that were negatively regulated by EGLN2 and KDM5A from RNA-seq. b, Venn diagram showing genes carrying the common CUT&RUN peaks at promoter regions that are negatively regulated by EGLN2 and KDM5A based on RNA-seq from panel a. c, Heat map of 48 directly target genes from panel b. d, Venn diagram showing overlapping of HIF1α bound peaks (n = 2755), H3P16oh/EGLN2, KDM5A and H3K4me3 overlapped peaks (n = 5053) and direct targets of EGLN2-H3P16oh-KDM5A-H3K4me3 signaling axis (n = 48) from MDA-MB-231 cells. e, Venn diagram showing overlap between HIF1/2α dependent genes(n = 368), EGLN2-KDM5A axis negatively regulation genes(n = 472) from RNA-Seq and direct targets of EGLN2-H3P16oh-KDM5A-H3K4me3 signaling axis(n = 48) in MDA-MB-231 cells. f, Venn diagram showing overlap between HIF1α direct genes(n = 150), EGLN2-KDM5A axis negatively regulated genes(n = 472) from RNA-Seq and direct targets of EGLN2-H3P16oh-KDM5A-H3K4me3 signaling axis(n = 48) in MDA-MB-231 cells. g, Venn diagram showing overlap between ADSL negative regulated genes (n = 1360) from RNA-Seq, EGLN2-KDM5A axis negatively regulated genes (n = 472) from RNA-Seq and targets of EGLN2-H3P16oh-KDM5A-H3K4me3 signaling axis(n = 48). h, qRT-PCR quantification of H3P16oh top ten target genes from MDA-MB-231 cells with EGLN2 or KDM5A depletion. The y axis shows averaged signals after normalization to Actin and then to siCtrl or shCtrl (n ≥ 3; mean ± s.d.; unpaired two-tailed Student’s t-test). *P < 0.05, **P < 0.01, ***P < 0.001. i, Screenshot of binding peak of HIF1α at DKK1 promoter in MDA-MB-231 cells. j, ARNT ChIP-qPCR to examine ARNT binding to promoter of DKK1, lgG and H3P16oh was set as negative and positive control. The y axis shows averaged signals after normalization to lgG (n = 3; mean ± s.d.; unpaired two-tailed Student’s t-test). *P < 0.05, **P < 0.01, ***P < 0.001.

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