YeastH3H4_submission3
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.  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.
Rules governing genomic nucleosome organization in the yeast genome