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

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

Research output: Contribution to journalArticle

472 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1073-1083
Number of pages11
JournalGenome research
Volume18
Issue number7
DOIs
StatePublished - Jul 1 2008

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Nucleosomes
Statistical Models
Yeasts
Genome
Genetic Promoter Regions
Genes
Saccharomyces cerevisiae
Transcription Factor TFIIB
Atlases
DNA Sequence Analysis

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., ... Pugh, B. F. (2008). A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome research, 18(7), 1073-1083. https://doi.org/10.1101/gr.078261.108
Mavrich, Travis N. ; Ioshikhes, Ilya P. ; Venters, Bryan J. ; Jiang, Cizhong ; Tomsho, Lynn P. ; Qi, Ji ; Schuster, Stephan C. ; Albert, Istvan ; Pugh, B. Franklin. / A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. In: Genome research. 2008 ; Vol. 18, No. 7. pp. 1073-1083.
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Mavrich, TN, Ioshikhes, IP, Venters, BJ, Jiang, C, Tomsho, LP, Qi, J, Schuster, SC, Albert, I & Pugh, BF 2008, 'A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome', Genome research, vol. 18, no. 7, pp. 1073-1083. https://doi.org/10.1101/gr.078261.108

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. / Mavrich, Travis N.; Ioshikhes, Ilya P.; Venters, Bryan J.; Jiang, Cizhong; Tomsho, Lynn P.; Qi, Ji; Schuster, Stephan C.; Albert, Istvan; Pugh, B. Franklin.

In: Genome research, Vol. 18, No. 7, 01.07.2008, p. 1073-1083.

Research output: Contribution to journalArticle

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AU - Ioshikhes, Ilya P.

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AU - Jiang, Cizhong

AU - Tomsho, Lynn P.

AU - Qi, Ji

AU - Schuster, Stephan C.

AU - Albert, Istvan

AU - Pugh, B. Franklin

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Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome research. 2008 Jul 1;18(7):1073-1083. https://doi.org/10.1101/gr.078261.108