Most nucleosomes are well-organized at the 5' ends of S. cerevisiae genes where 
"-1" and "+1" nucleosomes bracket a nucleosome-free promoter region (NFR). How 
nucleosomal organization is specified by the genome is less clear. Here we 
establish and inter-relate rules governing genomic nucleosome organization by 
sequencing DNA from more than one million immunopurified S. cerevisiae 
nucleosomes (displayed at http://atlas.bx.psu.edu/). Evidence is presented that 
the organization of nucleosomes throughout genes is largely a consequence of 
statistical packing principles. The genomic sequence specifies the location of 
the -1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which 
nucleosomes are packed, resulting in uniform positioning, which decays at 
farther distances from the barrier. We present evidence for a novel 3' NFR that 
is present at >95% of all genes. 3' NFRs may be important for transcription 
termination and anti-sense initiation. We present a high-resolution genome-wide 
map of TFIIB locations that implicates 3' NFRs in gene looping.