Extended Data Fig. 5: Genomic distribution of Kacme in fly and human cells by ChIP-seq and CUT&RUN, and the association of Kacme with increased transcription initiation.
From: Acetyl-methyllysine marks chromatin at active transcription start sites
a, ChIP-seq density of Kacme and H4Kac across Kacme ChIP-seq peaks. b, Colocalization of Kacme peaks with regions of enrichment from ChIP experiments from the MODENCODE database using the GenometriCorr colocalization ratio. c, Kacme ChIP-qPCR from two biological replicates after incubation of Kacme antisera with indicated competitor peptide at indicated concentrations. d, Comparison of binned Kacme ChIP-seq density with and without pre-incubation of Kacme antisera with H4Kac competitor peptide (75 nM). e, Comparison of binned Kacme ChIP-seq density with and without pre-incubation of Kacme antisera with H4Kacme competitor peptide (75 nM). f, Genome browser tracks of Kacme ChIP-seq after incubation of Kacme antisera with indicated competitor peptide (75 nM). g, Kacme and H4Kac ChIP-seq reads across transcription start sites (TSS) for all genes in K562 cells. h, Kacme, H4Kac, and H3K4me3 CUT&RUN density across TSS for all genes in K562 cells. i, Colocalization of Kacme peaks with regions of enrichment from ChIP experiments in human cells using the Interval Stats Ratio. j, Kacme ChIP-qPCR in HEK293T cells after incubation of Kacme antisera with indicated competitor peptide (75 nM). Bar plots show the mean of three biological replicates. Statistical analysis by two-tailed unpaired t-test. p < 0.0001; NS = not significant. k, Kacme ChIP-seq read counts in HEK293T cells after incubation of Kacme antisera with indicated competitor peptide (75 nM). Box plots show the distribution of mean read counts for each peak from three biological replicates. Distributions were compared using a two-tailed unpaired t-test. l, Relative gene-wide transcriptional activities as determined by TT-TL-seq. Normalized read counts were binned by the ratio of Kacme-to-H4Kac ChIP-seq signal. m, Relative transcriptional activity for genes in the 25th or 75th percentiles of Kacme levels as binned by H4Kac ChIP-seq signal. n, Estimates of the half-lives of promoter-proximal paused transcripts for genes in the 25th or 75th percentiles of Kacme levels determined by STL-seq. Data are binned by H4Kac ChIP-seq signal as in m. o, Relative promoter-proximal pause site occupancy as determined by STL-seq for genes in the 25th or 75th percentiles of Kacme ChIP-seq signal. Data is binned by H4Kac ChIP-seq signal. l-o, Distribution means compared with two-tailed unpaired Wilcoxon test for two biological replicates. k-o, 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 = 8429 (k), 4089 (l), 614 (m), 367 (n-o). p, HOMER motif analysis for promoters of genes with the highest ratios of Kacme over H4Kac ChIP-seq signal. Yellow boxes indicate enrichment of motifs associated with E2F family transcription factors.
