Rhabdomyosarcoma (RMS) is a pediatric tumor of skeletal muscle that resembles undifferentiated myogenic cells ( 5, 6). Analysis of the areas neighboring MyoD-bound sites revealed potential binding sites for a variety of other factors that are known or believed to play roles during myogenesis (e.g., Ap-1, Meis, Runx, and Sp1).
Genes that had increased expression with differentiation were associated with an increased MyoD ChIP-seq signal, and genes that decreased expression were associated with a decreased signal. We found that MyoD bound extensively both in undifferentiated, proliferating myoblasts and in terminally differentiated myotubes. In myogenic cells, MyoD heterodimerizes with members of the E-protein bHLH family, binds DNA in a sequence-specific fashion, and transactivates gene targets ( 4). MyoD is a member of the basic helix-loop-helix (bHLH) family of transcription factors, a large group of factors that bind DNA through a basic region and use amphipathic helices to heterodimerize with other bHLH proteins ( 2, 3). We have recently performed chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq) for the myogenic regulatory factor MyoD in murine cells of the skeletal muscle lineage and described widespread binding of MyoD in both intra- and intergenic regions of the genome ( 1). These results demonstrate that regional and local silencing of differentiation factors contributes to the differentiation defect in rhabdomyosarcomas. MEF2C is located in a genomic region that exhibits poor MyoD binding in RD cells, whereas JDP2 exhibits local DNA hypermethylation in its promoter in both RD cells and primary tumor samples.
These factors are expressed at lower levels in RD cells than muscle cells and rescue myogenesis when expressed in RD cells. Binding differences are found both across genomic regions and locally at specific sites that are associated with binding motifs for RUNX1, MEF2C, JDP2, and NFIC. Using MyoD chromatin immunoprecipitation coupled to high-throughput sequencing and gene expression analysis in both primary human muscle cells and RD rhabdomyosarcoma cells, we demonstrate that MyoD binds in a similar genome-wide pattern in both tumor and normal cells but binds poorly at a subset of myogenic genes that fail to activate in the tumor cells. Prior work has determined that DNA binding by MyoD occurs in the tumor cells, but myogenic targets fail to activate.
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