Wnt signalling controls the balance between stem cell proliferation and differentiation and patterning throughout development. Non-canonical Wnts, such as Wnt5a or Wnt11, enhance cardiac gene expression of endothelial progenitor cells (EPC), mesenchymal stem cells (MSC) and bone marrow mononuclear cells suggesting that non-canonical Wnts regulate cardiac commitment. However, the underlying mechanism is unclear. Using microarray analysis of Wnt5a-induced gene expression in EPC, we discovered that Wnt5a (1.0 μM, 24hours) significantly increased a variety of enzymes, which play key roles in epigenetic remodelling by modifying histone acetylation and methylation. Specifically, JMJD2B (205%), REST (311%), HDAC5 and HDAC7A (716 and 381%), YY1 (304%), and PCGF2 (352%), were significantly increased by Wnt5a. Wnt5a induced up-regulation of JMJD2B in EPC and MSC was further confirmed by real-time RT-PCR. The member of the JmjC-domain containing family, JMJD2B was recently shown to demethylate trimethylated histone H3 at lysine 9 (H3K9me3), thereby removing repressive histone modifications. Therefore, we hypothesized that increased JMJD2B might epigenetically modify gene expression, open chromatin structures at silenced promoters and modulate the differentiation of adult progenitor cells. Indeed, Wnt5a treatment reduced the repressive chromatin mark H3K9me3 as shown by Western blot and immunohistochemistry whereas global active chromatine marks (acetyl-H3 and trimethyl- H3K4) remained unchanged indicating that Wnt5a shifts the balance towards active gene expression. Furthermore, chromatin immunoprecipitation revealed that Wnt5a treatment increased the binding of JMJD2B at the promoter of the cardiac gene ANF. In line with removal of repressive chromatin marks, Wnt5a significantly increased differentiation of progenitor cells to cardiomyocytes. These data demonstrate that non-canonical Wnt5a induces epigenetic remodelling by removing repressive chromatin marks and may, thereby, sensitize adult progenitor cells for acquiring a cardiac cell fate. Further studies will investigate the specific contribution of the novel epigenetic modulator JMJD2B for adult stem cell functions.