We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes 
assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over 
Escherichia coli DNA, indicating that the yeast genome evolved to favor 
nucleosome formation. Many yeast promoter and terminator regions intrinsically 
disfavor nucleosome formation, and nucleosomes assembled in vitro show strong 
rotational positioning. Nucleosome arrays generated by the ACF assembly factor 
have fewer nucleosome-free regions, reduced rotational positioning and less 
translational positioning than obtained by intrinsic histone-DNA interactions. 
Notably, nucleosomes assembled in vitro have only a limited preference for 
specific translational positions and do not show the pattern observed in vivo. 
Our results argue against a genomic code for nucleosome positioning, and they 
suggest that the nucleosomal pattern in coding regions arises primarily from 
statistical positioning from a barrier near the promoter that involves some 
aspect of transcriptional initiation by RNA polymerase II.