We determined genome-wide nucleosome occupancies in mouse embryonic stem cells 
and their neural progenitor and embryonic fibroblast counterparts to assess 
features associated with nucleosome positioning during lineage commitment. 
Cell-type- and protein-specific binding preferences of transcription factors to 
sites with either low (Myc, Klf4 and Zfx) or high (Nanog, Oct4 and Sox2) 
nucleosome occupancy as well as complex patterns for CTCF were identified. 
Nucleosome-depleted regions around transcription start and transcription 
termination sites were broad and more pronounced for active genes, with distinct 
patterns for promoters classified according to CpG content or histone 
methylation marks. Throughout the genome, nucleosome occupancy was correlated 
with certain histone methylation or acetylation modifications. In addition, the 
average nucleosome repeat length increased during differentiation by 5-7 base 
pairs, with local variations for specific regions. Our results reveal regulatory 
mechanisms of cell differentiation that involve nucleosome repositioning.