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.
Mavrich
Travis N
TN
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Ioshikhes
Ilya P
IP
Venters
Bryan J
BJ
Jiang
Cizhong
C
Tomsho
Lynn P
LP
Qi
Ji
J
Schuster
Stephan C
SC
Albert
Istvan
I
Pugh
B Franklin
BF
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