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Fig. 3 | Genome Biology

Fig. 3

From: Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability

Fig. 3

ChIP-seq confirms enrichment of H4K20me3 at SAHF in senescent cells. a H4K20me3 enrichment at telomeric repeat sequences relative to DNA input (left) and histone H4 (right) in proliferating (PRO; blue) and RS (red) cells. The % mapped H4K20me3/% mapped control was calculated separately for each antibody and control. Mean value (n = 2) was plotted with standard error of the mean (SEM). b Quantitative PCR of H4K20me3 ChIP enrichment at 17p telomeres normalized to H4K20me3 ChIP enrichment at the β-globin locus in PRO and RS cells; error bars represent SEM of three experiments (two experiments with the Millipore 04–079 antibody and one experiment with the Cell Signalling 5737 antibody). c Quantitative PCR of H4K20me3 ChIP enrichment at 18q telomeres normalized to H4K20me3 ChIP enrichment at the β-globin locus in PRO and RS cells; error bars represent SEM of three experiments (as in panel b). d Total number of overlapping H4K20me3 peaks identified with both antibodies (intersection) in PRO and RS cells and significantly different (false discovery rate (FDR) <0.01) peaks between PRO and RS cells determined by DiffBind. e Total number of base pairs comprising H4K20me3 peaks identified with both antibodies (intersection) in PRO and RS cells and significantly different (FDR <0.01) peaks between PRO and RS determined by DiffBind. f Number of H4K20me3 DiffBind peaks from d that increase and decrease in RS cells relative to PRO cells. g Observed overlap and expected overlap (enrichment compared to random) between base pairs covered by RS H4K20me3 DiffBind peaks with base pairs covered by H3K9me3 peaks in senescent cells (empirical p < 0.001). h Observed overlap and expected (enrichment compared with random) overlap between base pairs covered by RS H4K20me3 peaks (intersection of both antibodies) with base pairs covered by H3K9me3 in senescent cells (empirical p < 0.001). i Mean RS and OIS H4K20me3 (normalized to histone H4) and OIS H3K9me3 (normalized to input) enrichment profiles (read count) at a composite H3K9me3 peak. j Observed/expected overlap (log2 fold enrichment compared with random) between base pairs covered by RS and OIS H4K20me3 peaks, RS H4K16ac peaks, DNA hypermethylated in RS regions, and DNA hypomethylated in RS regions with H3K9me3-marked late-replicating regions, H3K9me3-marked not late-replicating regions, and late-replicating regions not marked by H3K9me3. k Mean difference (RS − PRO) in H4K20me3 enrichment, H4K16ac enrichment, and percentage of methylated CpGs at a composite H3K9me3-marked late replicating region

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