Journal: Nature Communications

Article Title: DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes

doi: 10.1038/s41467-017-01724-9

Figure Lengend Snippet: Distinct DNA methylation patterns in A and B compartments in adult CM. Hi-C contact maps uncover topologically associated domains (TADs) and multi-TAD A/B compartments in adult CM. Principal component analysis characterizes the A/B status of compartments (A, PC1 > 0; B PC1 < 0). Histone modifications, CTCF, and the cohesion subunit (SMC1) (RPKM) predict the chromatin state. Presence of RNA expression (FPKM) and marking with H3K36me3, H3K27ac, H3K4me1, H3K4me3 classifies A compartments as active. The inactive chromatin status of B compartments is indicated by H3K9me3 enrichment. CpG methylation data (%) shows low-methylated regions (LMRs), characteristic for cis -regulatory elements, and partially methylated domains (PMDs) overlapping with A and B compartments, respectively. Non-CpG methylation (mCHH, %), and 5-hydroxymethylcytosine (5hmC, RPKM) mark A compartments. Data shown are from n = 3 Hi-C, n = 3 RNA-seq, n = 3 WGBS; n = 2 5hmC-seq and n = 1–2 ChIP-seq experiments. RPKM reads per kilobase per million, FPKM fragments per kilobase per million mapped reads

Article Snippet: The following antibodies were used in this study: CTCF (diagenode, C15410210-50, 4 µg/ChIP), Cohesin (anti-SMC1; biomol, A300-055A, 4 µg/ChIP), H3K9me1 (abcam, ab8896, 4 µg/ChIP), H3K9me2 (Cell Signaling Technology, #9753, 4 µg/ChIP), H3K9me3 (Diagenode, C15410193, 4 µg/ChIP).

Techniques: DNA Methylation Assay, Hi-C, RNA Expression, CpG Methylation Assay, Methylation, RNA Sequencing Assay, ChIP-sequencing