Gene expression frequently requires chromatin-remodeling complexes, and it is 
assumed that these complexes have common gene targets across cell types. 
Contrary to this belief, we show by genome-wide expression profiling that Bptf, 
an essential and unique subunit of the nucleosome-remodeling factor (NURF), 
predominantly regulates the expression of a unique set of genes between diverse 
cell types. Coincident with its functions in gene expression, we observed that 
Bptf is also important for regulating nucleosome occupancy at nucleosome-free 
regions (NFRs), many of which are located at sites occupied by the multivalent 
factors Ctcf and cohesin. NURF function at Ctcf binding sites could be direct, 
because Bptf occupies Ctcf binding sites in vivo and has physical interactions 
with CTCF and the cohesin subunit SA2. Assays of several Ctcf binding sites 
using reporter assays showed that their regulatory activity requires Bptf in two 
different cell types. Focused studies at H2-K1 showed that Bptf regulates the 
ability of Klf4 to bind near an upstream Ctcf site, possibly influencing gene 
expression. In combination, these studies demonstrate that gene expression as 
regulated by NURF occurs partly through physical and functional interactions 
with the ubiquitous and multivalent factors Ctcf and cohesin.