Chromatin immnunoprecipitation sequencing (ChIP-Seq) was performed on 20 mg cell lysate using the following antibodies: anti H3K4me3, Cat # 8580 Abcam; anti H3K27me3, Cat # 07-449, Millipore; anti H3K4me1, Cat # 5326, Cell Signaling; anti histone H3, Cat # 05-499, Millipore. ChIP library was constructed as described previously (Soleimani, V.D., et al., Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev Cell, 2012. 22(6): p. 1208-20.). Sequencing was done on Illumina GAIIX Genome Analyzer in duplicates. ChIP-Seq of Sox2 was performed by Chromatin Tandem Affinity Purification Sequencing as described previously (Soleimani, V.D., et al., Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev Cell, 2012. 22(6): p. 1208-20. Soleimani, V.D., et al., Chromatin tandem affinity purification sequencing. Nat Protoc, 2013. 8(8): p. 1525-34) . Briefly, to produce the TAP-tagged fusion construct mouse Sox2 gene was fused with a C-terminal TAP tag (6XHIS-TEV-3FLAG) and inserted into Sox2 locus using homologous recombination in G4 ES cell line (G4-129S6B6F1, Samuel Lunenfeld Research Institute, Mount Sinai Hospital). ES cells harboring the recombinant knocked-in allele of Sox2 was grown on Mitomycin C treated MEFs in the presence of LIF. RNA-Seq: Total RNA was extracted from primary myoblasts or differentiated myotubes over expressing and empty vector retroviral construct (48 hours differentiation) as described previously (Soleimani, V.D., et al., Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis. Mol Cell, 2012. 47(3): p. 457-68.).