Extended Data Fig. 1: Reproducibility analysis of the biological replicates for the H3T11ph ChIP-seq.
From: Nuclear-localized pyruvate kinases control phosphorylation of histone H3 on threonine 11
(a) Correlation analysis of the biological replicates of the H3T11ph ChIP-seq analysis of Col-0 under glucose depletion and stimulation. The x and y axes indicate the read coverage normalized to the total mapped reads, and values are in the log2 scale. (b) Scatterplot of H3T11ph-occupied loci downregulated in Col-0 under glucose depletion vs. glucose stimulation. The x-axis indicates log2-normalized ChIP read counts, and the y-axis indicates the log2 fold change of H3T11ph levels. The dashed line indicates a fold change of 1.5. Significant (FDR < 0.05) up- and downregulated peaks are marked in red and blue, respectively. The up- and downregulated loci are indicated. (c) Metagene plots of H3T11ph enrichment in Col-0 under glucose depletion and stimulation. The log2 ratio of normalized enrichment (H3T11ph/Input) for each gene region, including the 2-kbp upstream and downstream regions from the gene, was used for the average gene analysis. The transcription start site (TSS) and transcription termination site (TTS) are indicated. (d) ChIP–seq for H3T11ph in Col-0 under glucose depletion and stimulation. The genome-browser track views are shown (chr3: 9,391,000–9,638,000 and chr4: 14,036,000–14,302,000).
