Table 1.
A compilation of information on different histone modifications and chromatin-modifying enzymes, indicating where they have been analyzed in the cardiac system or associated with cardiac disease
| Marks | cis-Regulatory elements | Genome-wide studies in cardiac cells | Modifiers | Associations with heart defects/disease |
|---|---|---|---|---|
| Histone modifications | ||||
| H3K9ac | Active promoters | Adult hearts (Sayed et al. 2013) HL-1 cells (Schlesinger et al. 2011) |
HATs (p300/CBP; GCN5/PCAF) HDACs |
p300 (Han et al. 2011) HDAC classes I, II, III (Han et al. 2011; Lara-Pezzi et al. 2012) |
| H3K18ac | Active promoters | |||
| H3K27ac | Enhancers or promoters | Differentiating ESCs (Wamstad et al. 2012) | ||
| H4ac (H4K5K8K12K16) | Active promoters and gene bodies | HL-1 cells (Schlesinger et al. 2011) | ||
| H3K4me1 | Promoters and enhancers | Differentiating ESCs (Wamstad et al. 2012) | HMTs | WHSC1 (H3K36me3) (Nimura et al. 2009) |
| H3K4me2 | Active promoters and gene bodies | HL-1 cells (Schlesinger et al. 2011) | ||
| H3K4me3 | Active promoters (at transcription start sites) | Differentiating ESCs (Paige et al. 2012; Wamstad et al. 2012) HL-1 cells (Schlesinger et al. 2011) |
MLL2 (H3K4me) (Ng et al. 2010) EZH2 (H3K27me) (Delgado-Olguin et al. 2012) |
|
| H3K9me2 | Inactive promoters | PTIP (H3K4me) (Stein et al. 2011) | ||
| H3K27me3 | Inactive promoters | Differentiating ESCs (Paige et al. 2012; Wamstad et al. 2012) | HDMs | JARID2, UTX (H3K27), JMJD2 (Lara-Pezzi et al. 2012) |
| H3K36me3 | Active gene bodies | Differentiating ESCs (Paige et al. 2012) | ||
| H3K4me1 + H3K27me3 no H3K27ac | Poised enhancers | Differentiating ESCs (Wamstad et al. 2012) | ||
| Histone variants, H3.3, H2A.Z | Enhancers | |||
| Other chromatin-modifying enzymes | ||||
| Poly(ADP-ribose) polymerases | Bind DNA breaks and regulate transcription | PARP-1 (Han et al. 2011) | ||
| ATP-dependent chromatin remodeler, e.g., SWI/SNF, ISWI, CHD | Alter nucleosomes structure | BAF, BRG1, CHD7, BAF45c/DPF3 (Han et al. 2011) | ||
| RNA polymerase II (Ser5Phos) | Proximal promoters (at transcription start sites) and low at enhancers | Adult hearts (Sayed et al. 2013) Differentiating ESCs (Wamstad et al. 2012) |
||
| DNA modifications | ||||
| 5mC at CpG islands | Inactive promoters | Mothers with CHD pregnancy (Chowdhury et al. 2011) | Chowdhury et al. 2011 | |
| 5hmC | Active promoters, genes, and enhancers | |||
HAT, histone acetyltransferase; HDAC, histone deacetylase; ESC, embryonic stem cell; HMT, histone methyltransferase; HDM, histone demethylase; CHD, congenital heart disease.