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. Author manuscript; available in PMC: 2020 Aug 18.
Published in final edited form as: Cell Rep. 2019 Jun 18;27(12):3522–3532.e3. doi: 10.1016/j.celrep.2019.05.062

Figure 4. KDM1A Functions at Active Enhancers to Remove H3K4me2.

Figure 4.

(A) Binned distances between nearest GRBS and TSSs of Dex-induced (Dex-up), Dex-repressed (Dex-dw), or Ctl genes.

(B) Fraction of genes with a GRBS or control region ± 25 kb or ± 50 kb from the TSS for each gene group. UpCoReg, Dex-induced GR-KDM1A coregulated genes; DwCoReg, Dex-repressed GR-KDM1A coregulated genes.

(C and D) ChIP-seq KDM1A density (C) and H3K4me2 LFC (D) at the TSS of control genes (Ctl TSS), Dex-up genes (Up TSS), Dex-dw genes (Dw TSS), and GRBSs ± 25 kb of a Dex-up gene (Up GRBS). E, EtOH; D, Dex. Density quantified ± 250 bp from TSS or GRBS center. See also Figure S4A.

(E) KDM1A density after Dex at TSSs or Up GRBSs parsed by genes that are co-regulated (CoReg) or not co-regulated (Not) as defined in Figure 1A.

(F and G) H3K27ac ChIP-seq density (F) and LFC (G) at parsed GRBSs as in Figure 3C. TSSs of control genes are included for reference. See also Figures S4B and S4C.

(H) GRBSs ± 25 kb from the TSS of a Dex-responsive gene parsed by KDM1A status, as in Figure 3C. Odds ratio over control regions is plotted.

All ChIP-seq p values from Bonferroni-corrected pairwise Mood’s median test.