DOI: 10.1101/gr.078261.108. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

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

10.1101/gr.078261.108

Crossref journal-article

Cold Spring Harbor Laboratory

Genome Research (246)

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.

Bibliography

Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I., & Pugh, B. F. (2008). A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research, 18(7), 1073â1083.

Authors 9

Travis N. Mavrich (first)
Ilya P. Ioshikhes (additional)
Bryan J. Venters (additional)
Cizhong Jiang (additional)
Lynn P. Tomsho (additional)
Ji Qi (additional)
Stephan C. Schuster (additional)
Istvan Albert (additional)
B. Franklin Pugh (additional)

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Dates

Type	When
Created	17 years, 2 months ago (June 12, 2008, 9:26 p.m.)
Deposited	3 years, 9 months ago (Nov. 18, 2021, 2:54 p.m.)
Indexed	1 week, 3 days ago (Aug. 19, 2025, 5:57 a.m.)
Issued	17 years, 2 months ago (June 12, 2008)
Published	17 years, 2 months ago (June 12, 2008)
Published Online	17 years, 2 months ago (June 12, 2008)
Published Print	17 years, 1 month ago (July 1, 2008)

Funders 0

None

BibTeX

@article{Mavrich_2008, title={A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome}, volume={18}, ISSN={1088-9051}, url={http://dx.doi.org/10.1101/gr.078261.108}, DOI={10.1101/gr.078261.108}, number={7}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Mavrich, Travis N. and Ioshikhes, Ilya P. and Venters, Bryan J. and Jiang, Cizhong and Tomsho, Lynn P. and Qi, Ji and Schuster, Stephan C. and Albert, Istvan and Pugh, B. Franklin}, year={2008}, month=jun, pages={1073–1083} }

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