A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
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.
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Travis N
TN
Mavrich
Ilya P
IP
Ioshikhes
Bryan J
BJ
Venters
Cizhong
C
Jiang
Lynn P
LP
Tomsho
Ji
J
Qi
Stephan C
SC
Schuster
Istvan
I
Albert
B Franklin
BF
Pugh
D020413:3' Untranslated Regions / Q000235:genetics; D002874:Chromosome Mapping / Q000706:statistics & numerical data*; D015825:Chromosomes, Fungal / Q000235:genetics*; D004271:DNA, Fungal / Q000032:analysis; D016681:Genome, Fungal; D008957:Models, Genetic; D009707:Nucleosomes / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*
D020413:3' Untranslated Regions; D004271:DNA, Fungal; D009707:Nucleosomes