Fig. 6: ChIP-iDEMS measures DNA modifications on histone PTM-associated DNA.
From: Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS
a, Schematic of strategy for mass spectrometry analysis of EdU-labelled, immunoprecipitated DNA. b, Methylation levels in H4K20me2-, H4K20me0- and H4K5ac-associated DNA, compared with gDNA. c, Methylation levels in H3K9me3- and H3K36me3-associated DNA, compared with gDNA. d, Methylation levels in H4K20me2-, H4K20me0- and H4K5ac-associated EdU+ ssDNA, compared with EdU+ ssDNA. e, Methylation levels in H3K9me3- and H3K36me3-associated EdU+ ssDNA, compared with EdU+ ssDNA. f, iDEMS opens new avenues for understanding DNA modifications. In b–e, data are presented as mean ± s.d. from three biological replicates. P values calculated using one-way ANOVA, adjusting for multiple comparisons: *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001. Exact adjusted P values for b: total gDNA versus H4K20me2 DNA: P = 0.0758; total gDNA versus H4K20me0 DNA: P = 0.9522; total gDNA versus H4K5ac DNA: P = 0.0298. Exact adjusted P values for c: total gDNA versus H3K9me3 DNA: P < 0.0001; total gDNA versus H3K36me3 DNA: P = 0.0001. Exact adjusted P values for d: EdU+ ssDNA versus H4K20me2 DNA: P = 0.9987; EdU+ ssDNA versus H4K20me0 DNA: P = 0.0035; EdU+ ssDNA versus H4K5ac DNA: P = 0.0175. Exact adjusted P values for e: EdU+ ssDNA versus H3K9me3 DNA: P < 0.0001; EdU+ ssDNA versus H3K36me3 DNA: P = 0.6637. Numerical source data are provided.
