Extended Data Fig. 7: H4Kacme ChIP-seq in human cells supports conclusions from Kacme ChIP-seq, and the relationship of Kacme with KATs and the in vitro acetylation of H4 peptides.
From: Acetyl-methyllysine marks chromatin at active transcription start sites
a, Genome browser tracks of Kacme and H4Kacme ChIP-seq from two biological replicates. b, ENCODE transcription factor enrichment analysis for genes marked by H4Kacme. Yellow boxes indicate enrichment of motifs associated with E2F family transcription factors. c, KEGG pathways that are enriched for genes marked by H4Kacme. d, MSigDB pathways that are enriched for genes marked by H4Kacme. e, Relative gene-wide transcriptional activities as determined by TT-TL-seq. Normalized read counts were binned by the ratio of H4Kacme-to-H4Kac ChIP-seq signal. f, Relative transcriptional activity for genes in the 25th or 75th percentiles of H4Kacme levels as binned by H4Kac ChIP-seq signal. g, Estimates of the half-lives of promoter-proximal paused transcripts for genes in the 25th or 75th percentiles of H4Kacme levels determined by STL-seq. Data are binned by H4Kac ChIP-seq signal as in f. h, Relative promoter-proximal pause site occupancy as determined by STL-seq for genes in the 25th or 75th percentiles of H4Kacme ChIP-seq signal. Data is binned by H4Kac ChIP-seq signal. e-h, Distribution means compared with two-tailed unpaired Wilcoxon test for two biological replicates. The box plots indicate the median (centre line), the third and first quartiles (box limits), 1.5x interquartile range (IQR) above and below the box (whiskers), and the 95% confidence interval (notches). Outlier points are not plotted. * p < 0.05; *** p < 0.001; NS = not significant. n = 2876 (e), 430 (f), 285 (g-h). i, ENCODE transcription factor enrichment analysis of genes marked by Kacme using Enrichr56. Yellow boxes indicate enrichment of motifs associated with p300. j, ChIP-seq density of p300 (SRX150481) across Kacme ChIP-seq peaks. k, p300 ChIP-qPCR enrichment at selected loci identified by Kacme ChIP-seq. Bar plot shows the mean of three biological replicates of HEK-293T cells, and error bars show standard deviation. Statistical analysis by two-tailed unpaired t-test. * p < 0.05; ** p = 0.007. GD = gene desert. l-m, Extracted ion chromatograms of H4 (l) and H4Kac (m) peptides after in vitro acetylation by p300. n-o, Extracted ion chromatograms of H4 (n) and H4Kac (o) peptides after in vitro acetylation by Tip60. Extracted ion chromatograms of H4Kac (m, o) are representative of all acetylated species. p, Extracted ion chromatograms for H4Kme1 peptides after in vitro acetylation with p300 or Tip60. Note that unlike H4 peptides, the majority of H4Kme1 peptides are not consumed in the reaction, suggesting H4K peptides are better substrates for p300 than H4Kme1 peptides. q, Kacme dot blot of H4Kme1 and H3K27me1 peptides after in vitro acetylation with p300. Data represent two independent experiments. Yellow boxes indicate Kacme peptides.
