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. Author manuscript; available in PMC: 2017 Jul 12.
Published in final edited form as: Cell Rep. 2016 Sep 27;17(1):289–302. doi: 10.1016/j.celrep.2016.08.083

Figure 1. Alterations of DNA Methylation Cause Selective Genome-wide Changes in Histone Modifications.

Figure 1

(A) Schematic of experimental design. Wild-type, TKO, DKO, and Dnmt Reconstitution cell lines each are assayed for DNA methylation by RRBS, histone modifications by ChIP-seq, and gene expression using RNA-seq.

(B) Left: mass spectrometry measurement of global 5mC levels between WT (n = 6), TKO (n = 7), TKO+Dnmt3a1 (n = 5), TKO+Dnmt3a2 (n = 6), TKO+Dnmt3b1 (n = 4), and DKO and reconstitution cell lines (n = 2). Data are represented as mean ± SEM. Right: global 5mC levels measured by RRBS.

(C) Global Pearson correlation analysis between H3K27me3, H3K4me1, H3K4me3, and H3K27ac histone modifications across mESC lines. Correlation was calculated based on 1 kb genome-wide bins.

(D) Genome browser tracks of RRBS and histone modification ChIP-seq between WT, KO, and Dnmt reconstitution mESC lines. Regions of interest exhibiting histone modification changes are boxed.