Genome-wide measurement of gene expression changes with Bptf knockout in mouse embryonic fibroblasts

Gene expression frequently requires the action of chromatin remodeling complexes and it is assumed that these complexes have common gene targets across cell-types. Contrary to this belief, we show that Bptf, an essential and unique subunit of the Nucleosome Remodeling Factor (NURF), largely regulates cell-type-restricted gene expression across diverse cell-types. Unexpectedly, cell-type-restricted gene expression is accomplished through both physical and functional interactions between NURF and the ubiquitous multivalent factor Ctcf. We go on to show in these cell types, that Bptf influences the regulatory activity of Ctcf binding sites in a cell type-restricted manner. Detailed studies of Ctcf binding sites in embryonic stem cells (ESC) show that Bptf prevents Klf4 binding upstream of H2-K1, and facilitates RNA polymerase elongation through Ccnd1, to regulate genes important for embryonic development. In total, these studies provide mechanisms by which prominent chromatin remodeling complexes can maintain cell-type-restricted gene expression through ubiquitous factors like Ctcf. Analysis of gene expression changes in mouse embryonic cells with Bptf knockout using TetO-Cre expression system. Three independent cell lines with knockout or control genotypes were depleted of Bptf prior to extracting total RNA for microarray analysis.