RT Journal
A1 Mavrich, Travis N.
A1 Ioshikhes, Ilya P.
A1 Venters, Bryan J.
A1 Jiang, Cizhong
A1 Tomsho, Lynn P.
A1 Qi, Ji
A1 Schuster, Stephan C.
A1 Albert, Istvan
A1 Pugh, B. Franklin
T1 A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
JF Genome Research 
JO Genome Research 
YR 2008 
FD July 01 
VO 18 
IS 7 
SP 1073 
OP 1083 
DO 10.1101/gr.078261.108 
UL http://genome.cshlp.org/content/18/7/1073.abstract 
AB 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.