To identify Bptf-dependent gene targets we employed a microarray based approach on Bptf knockout ES cells during the early stages of differentiation and an embryoid body model. We discovered a role for Bptf in the regulation of gene clusters essential for development, morphogenesis, nervous system development and cell death and proliferation. Interestingly many transcription factors, primarily the homeobox-containing genes, are dependent on Bptf for their proper repression during undifferentiated and differentiated states. This dependence is interesting as NURF has been shown to be a activator of Hox gene transcription in more differentiated tissues in Drosophila and the mouse [13],[15]. As expected many markers of ectoderm (Nestin, Fgf5), mesoderm (Gsc, Lhx1, Fgf8, Tbx6, Wnt3) and endoderm (Lefty1, Cer1, Nodal, Hesx1) cell lineages require Bptf for their expression. These gene targets corroborate well with those identified from our in vivo studies on Bptf mutant embryos further supporting the conclusion that Bptf is essential for the development of ectoderm, mesoderm and endoderm. This also suggests that our microarray dataset obtained from ES cells is a reasonable approximation of the expression defects occurring in Bptf mutant embryos in vivo.
