Leonardo Meza-Zepeda and colleagues report the genomic and epigenomic profiles of a mesenchymal stem cell (MSC) line before and after differentiation to the osteogenic lineage (Stem Cells doi:10.1002/stem.1759, 4 June 2014). Using RNA sequencing, they found 1,462 genes upregulated and 1,695 genes downregulated 28 days after differentiation was initiated. A master regulator of osteogenesis, RUNX2, was among the significantly upregulated genes in their data set. They subsequently performed genome-wide profiling of RUNX2 binding sites, identifying 8,871 candidate sites and 2,166 target genes in MSCs differentiated in vitro. Among the binding sites were 97 microRNA genes, 824 cancer-related genes and 467 genes related to growth and proliferation. They further validated RUNX2 binding sites in primary NHOst osteoblasts. They also documented epigenetic changes through chromatin immunoprecipitation and sequencing (ChIP-seq) for five histone modifications, finding that trimethylation of lysine 4 on histone H3 (H3K4me3) was the most common differentially regulated histone modification. Finally, through filtering of candidate regions and in vitro silencing experiments, they identified TEAD2 and GTF2I as novel regulators of osteogenesis. These data provide an important resource for researchers studying osteogenic differentiation and bone cancer development.