Ted to form stable heterochromatin histone marks over methylated DNA [47, 48]. Additionally
Ted to form stable heterochromatin histone marks over methylated DNA [47, 48]. Additionally, MBD3 is enriched at active promoters (with a positive correlation with H3K4me3) and at the enhancers of active genes that are usually H3K4me1 marked [49, 50]. Indirect interactions between MBDs and H3K4 methylation can also be hypothesized, i.e. ZIC2, an enhancer-binding factor which colocalizes H3K4me1 and the other enhancer marks (P300, H3K27ac) is shown to interact with MBD3/NURD in mouse ESCs [51]. Thus, the MBDs PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28993237 could be effectors of the crosstalk between DNA methylation and the H3K4me1 and H3K4me3 interaction observed here. Therefore, to check the MBD effectors hypothesis we compared the chromatin immunoprecipitation sequencing (ChIP-seq) profiles of the MBD proteins for which data is available: MBD1A/B, MBD2, MBD3, MBD4 andSharifi-Zarchi et al. BMC Genomics (2017) 18:Page 7 ofacebdfghiFig. 2 (See legend on next page.)Sharifi-Zarchi et al. BMC Genomics (2017) 18:Page 8 of(See figure on previous page.) Fig. 2 Distinct deposition of H3K4me1 from the other active chromatin marks. The regulatory sites are sorted according to their DNA methylation level in ESCs from 0 to 100 methylated. Average enrichment of different chromatin marks (rows) over sites of the same DNA methylation level are shown with (a) color bars and (b) lines (for the seven active chromatin marks). Average enrichments are scaled to have equal maximum for different marks. Pairwise scatter plots of DNA methylation versus RNA transcription for promoters (c) and enhancers (d). The scattering density is shown in green. Red and blue dots show sites with DNA methylation lower or higher that 50 , respectively. Cyan spreads show promoter sites and Mdivi-1 web magenta circles show the promoters whose transcription is more than 4 in log2 scale. (e) Heat map of hypermethylated enhancers (DNA methylation >75 ) and expressed transcripts (transcription >4 in log2 scale). To adjust the color codification, the DNA methylation, percentages are multiplied by 0.1, and H3K4me2 and H3K4me2 peaks by 5, the RNA-seq values are in log2 scale. Higher values correspond to redder color. The table to the right annotates Gene Ontology (GO) terms: E (Enzymatic activity) in green and C (Chromatin organization regulation) in magenta. H3K4 methylation, me3 (f), me2 (g) and me1 (h), enrichments within regulatory sites versus DNA methylation. Each point represents a single regulatory site. Each point represents a single regulatory site. The scattering density is shown in green. Red and blue dots show sites with DNA methylation lower or higher that 50 , respectively. Cyan spreads show promoter sites and magenta circles show the promoters whose transcription is more than 4 in log2 scale. The over imposed black lines mark the median of the H3K4 methylations smoothed using a robust loess regression. (i) DNA methylation and enrichment of the seven active chromatin marks around the Myc and Sox2 gene loci. The location of all known putative Myc and Sox2 enhancers taken from the supplemental material of Shen et al. [45] and from PHANTOM5 [46], are marked by red bars at the bottom. The y-axis represents the DNA methylation measured as the percentage of reads that support the methylated state of each CpG (estimated methylation level). For each histone mark track and for the Pol2 and P300 tracks, the y-axis represents the normalized level of ChIP-seq signal over the genomic regionsMECP2 (Table 1, row 11) with enrichment sites of H3K4.