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PMID: 18550805 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

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

Genome research ·Vol. 18 ·No. 7 ·2008-07-00 ·Pages 1073-83

Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF

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.

MeSH Terms
3' Untranslated Regions/genetics Chromosome Mapping/statistics & numerical data Chromosomes, Fungal/genetics DNA, Fungal/analysis Genome, Fungal Models, Genetic Nucleosomes/genetics Promoter Regions, Genetic Saccharomyces cerevisiae/genetics
Chemicals
3' Untranslated Regions DNA, Fungal Nucleosomes
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Mavrich Travis N
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Ioshikhes Ilya P
Venters Bryan J
Jiang Cizhong
Tomsho Lynn P
Qi Ji
Schuster Stephan C
Albert Istvan
Pugh B Franklin
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.078261.108
Published
2008-07-00
Epub
2008-00-12
Pages
1073-83
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC2493396
Subset
IM
Grants
NHGRI NIH HHS · R01 HG004160 · United States
NHGRI NIH HHS · HG004160 · United States
External Links
PubMed source DOI: 10.1101/gr.078261.108 PMC Full Text View journal details
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