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. 2022 Sep 12;50(17):9797–9813. doi: 10.1093/nar/gkac744

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© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — KdmB, EcoA, RpdA and SntB co-localized at thousands of promoters (A) A VENN diagram showing the number of common and unique genes between KdmB^HA, EcoA^HA, RpdA^HA and SntB^HA. (B) Genome-browser screenshots showing the binding location of KdmB^HA, EcoA^HA, RpdA^HA and SntB^HA. (C) Heatmaps displaying binding locations, signals and intensities of KdmB^HA, EcoA^HA, RpdA^HA and SntB^HA over their overall target genes (n = 4165). (D) A pie chart showing the distribution of the common KERS binding sites at distal promoters, proximal promoters, genic regions (exon/intron) and gene ends. (E, F) Heatmaps displaying ChIPseq signals of (E) KdmB^HA, histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 9 acetylation (H3K9ac), histone H3 lysine 27 acetylation, histone H3, (F) TBP^HA and TFIIB^HA at the –3 kb to + 3 kb region with respect to the start codon (ATG) of KERS target genes. (G) A line graph showing the median binding signals of KdmB^HA, EcoA^HA, RpdA^HA, SntB^HA, TBP^HA and TFIIB^HA at the –2 kb to + 2 kb region with respect to the start codon (ATG) of KERS target genes. (H) A scatter plot showing the correlation between KdmB bindings at promoters and Pol II occupancies at coding regions. (I) A line plot showing the median Pol II ChIPseq signals between 2 kb upstream (–2 kb) of the translational start codon (ATG) to 1 kb downstream (+1 kb) of the translational stop codon of expressed genes in the WT and mutant strains deleted (Δ) or depleted (TetON) for the indicated subunit. The asterisk (*) indicates strains grown under the same experimental conditions for protein expression shutdown by the TetON system. (J) Heatmap plots showing binding locations, signals and intensities of KdmB^HA, EcoA^HA, RpdA^HA and SntB^HA in WT, kdmBΔ or sntBΔ background. (K) Genome-browser screenshots showing binding of KdmB^HA, EcoA^HA, RpdA^HA and SntB^HA in WT (+), kdmBΔ or sntBΔ background.