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A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.


Mavrich TNTravis N , Ioshikhes IP Ilya P , Venters BJ Bryan J , Jiang C Cizhong , Tomsho LP Lynn P , Qi J Ji , Schuster SC Stephan C , Albert I Istvan , Pugh BF B Franklin . Genome research. 2008 7 ; 18(7). 1073-83


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 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.