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Venters Lab

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

AUTHORS

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

ABSTRACT

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.