Figure 3

MSC binding is associated with open chromatin. (A) Sites bound by MyoD and MSC are associated with acetylated histones. ChIP-seq for acetylated histone H4 (AcH4) was performed in RD cells and density plots constructed to compare the square root of the AcH4 value at all sites bound by MSC, MyoD or both factors. (B) MSC-specific and MyoD/MSC shared peaks are associated with higher levels of AcH4 near the transcription start site (TSS) of genes compared to MyoD-specific peaks. Density plots were constructed as in (A) for categories of peaks first split by peak identity (MyoD, MSC, shared), then subcategorized on distance from the nearest TSS. (C) Sites bound by MSC in RD cells overlap with DNase hypersensitive (HSS) sites in normal human myoblasts. Publicly available DNase HSS data from human myotubes were compared to the sites bound by MyoD and MSC in RD cells. Data for each factor category (for example, MSC-specific) are plotted as the fraction of peaks that overlap with locations that have a signal in the HSS data (that is, the graphed fraction = 1 – fraction of peaks at HSS score of ‘0’). AcH4, acetylated histone H4; bHLH, basic helix-loop-helix; ChIP, chromatin immunoprecipitation; ChIP-seq, chromatin immunoprecipitation coupled to high-throughput sequencing; HSS, hypersensitive; K, thousands of bp; MSC, musculin; TSS, transcription start site.