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

  1. Travis N. Mavrich1,2,
  2. Ilya P. Ioshikhes3,
  3. Bryan J. Venters1,2,
  4. Cizhong Jiang1,2,
  5. Lynn P. Tomsho2,
  6. Ji Qi2,
  7. Stephan C. Schuster2,
  8. Istvan Albert2, and
  9. B. Franklin Pugh1,2,4
  1. 1 Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
  2. 2 Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
  3. 3 Department of Biomedical Informatics and Molecular & Cellular Biochemistry, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA

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.

Footnotes

  • 4 Corresponding author.

    4 E-mail bfp2{at}psu.edu; fax (814) 863-7024.

  • [Supplemental material is available online at www.genome.org.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.078261.108.

    • Received March 9, 2008.
    • Accepted April 15, 2008.

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