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Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Identification and Nomenclature of the Consensus Nucleosomes Across the Yeast Genome

The nucleosome particle is the basic repeating unit of eukaryotic chromatin structure. Packaging DNA into nucleosomes alters sequence accessibility. As a consequence, the positioning of nucleosome along chromatin influences a variety of biological processes. A genome-wide map of nucleosome positions is essential to understand the impact of nucleosome positioning on gene expression. Recently, five high-resolution genome-wide maps of nucleosome locations in yeast have been produced by tiling array or high-throughput sequencing technology. All reveal strong canonical positioning around the transcriptional start site (TSS). However, there is no standard for identifying nucleosome positions relative to the TSS. This may create confusion and inconsistencies when referring to individual nucleosomes or canonical positions, particularly if nucleosomes have different functions at different positions. Here, we generated a complete reference position map of consensus nucleosomes in yeast derived from six independent experimental determinations, and introduce the first systematic scheme to label the nucleosomes. These consensus nucleosomes serve as a reference map. The distribution profile of the reference nucleosomes around TSS is consistent with experimentally derived nucleosomes. A nucleosome browser was constructed to view and compare the reference nucleosomes and other published nucleosomes. Applying the labeling scheme, we reconfirm changes in nucleosome occupancy in promoter regions in response to heat shock and in yeast mutants. In addition to this, we developed a retrieval system for reference nucleosomes allowing users to extract the reference nucleosomes in a given region or a list of genes. This approach can be also applied to other species and facilitate sharing of the high-throughput data and scientific communication.

References and Footnotes
  1. Lee, W., Tillo, D., Bray, N., Morse, R.H., Davis, R.W., Hughes, T.R. and Nislow, C. (2007) A High-Resolution Atlas of Nucleosome Occupancy in Yeast. Nature Genetics, 39, 1235-1244.
  2. Whitehouse, I., Rando, O.J., Delrow, J. and Tsukiyama, T. (2007) Chromatin Remodelling at Promoters Suppresses Antisense Transcription. Nature, 450, 1031-1035.
  3. Mavrich, T.N., Ioshikhes, I.P., Venters, B.J., Jiang, C., Tomsho, L.P., Qi, J., Schuster, S.C., Albert, I. and Pugh, B.F. (2008) A Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Throughout the Yeast Genome. Genome Research, 18, 1073-1083.
  4. Field, Y., Kaplan, N., Fondufe-Mittendorf, Y., Moore, I.K., Sharon, E., Lubling, Y., Widom, J. and Segal, E. (2008) Distinct Modes of Regulation by Chromatin Encoded Through Nucleosome Positioning Signals. PLoS Computational Biology, 4, e1000216.
  5. Shivaswamy, S., Bhinge, A., Zhao, Y., Jones, S., Hirst, M. and Iyer, V.R. (2008) Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation. PLoS Biology, 6, e65.

Cizhong Jiang
B. Franklin Pugh

Ctr for Eukaryotic Gene Regulation
Dept of Biochemistry and
Molecular Biology
Pennsylvania State Univ.
University Park, PA 16802
USA

bfp2@psu.edu
cuj5@psu.edu