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. Author manuscript; available in PMC: 2022 Apr 1.
Published in final edited form as: Cell Rep. 2022 Mar 15;38(11):110524. doi: 10.1016/j.celrep.2022.110524

Figure 7. Double-knockout cells further increase pro-differentiation gene expression and H3K4me3 signal.

Figure 7.

(A) Volcano plots of log2 fold change of transcripts expressed in Z11Z131Δ cells versus WT, Zbtb11, and Zbtb131Δ cells grown in the absence of doxycycline for 3 days in +2i + LIF media (n = 3). Significant changes are marked in orange. Double knockout of Zbtb11 and Zfp131 mutations in ESCs induce further aberrant gene expression.

(B) The log2 fold change of developmentally regulated TFs obtained from bulk RNA-seq experiment in Z11Z131Δ cells versus WT, Zbtb11Δ, and Zfp131Δ in +2i + LIF and −2 + LIF conditions (n = 3). Z11Z131Δ mutations induced higher expression of TFs associated with all three embryonic layers compared with single knockout lines.

(C) Metagene plots for NELF signal difference in ZBTB11 only, ZFP131 only, and co-bound regions in double knockout versus WT (n = 2 for all). ZBTB11 and ZFP131 sites lose NELF in Z11Z131Δ cells. All comparisons were done in −2i + LIF.

(D) Metagene plots for H3K4me3 signal distribution at ZBTB11, ZFP131, and co-occupied genes in Z11Z131Δ cells versus WT (n = 2 for all). All comparisons were done in −2i + LIF. TTS, transcription termination site.

See also Figures S11 and S12.