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Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
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| Title: | Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences? |
| Authors: | Stein, Arnold Browse this author | | Takasuka, Taichi E. Browse this author | | Collings, Clayton K. Browse this author |
| Issue Date: | 1-Jan-2010 |
| Publisher: | Oxford University Press |
| Journal Title: | Nucleic Acids Research |
| Volume: | 38 |
| Issue: | 3 |
| Start Page: | 709 |
| End Page: | 719 |
| Publisher DOI: | 10.1093/nar/gkp1043 |
| Abstract: | ABSTRACT: Large-scale and genome-wide studies have concluded that ∼80% of the yeast (Saccharomyces cerevisiae) genome is occupied by positioned nucleosomes. In vivo this nucleosome organization can result from a variety of mechanisms, including the intrinsic DNA sequence preferences for wrapping the DNA around the histone core. Recently, a genome-wide study was reported using massively parallel sequencing to directly compare in vivo and in vitro nucleosome positions. It was concluded that intrinsic DNA sequence preferences indeed have a dominant role in determining the in vivo nucleosome organization of the genome, consistent with a genomic code for nucleosome positioning. Some other studies disagree with this view. Using the large amount of data now available from several sources, we have attempted to clarify a fundamental question concerning the packaging of genomic DNA: to what extent are nucleosome positions in vivo determined by histone-DNA sequence preferences? We have analyzed data obtained from different laboratories in the same way, and have directly compared these data. We also identify possible problems with some of the experimental designs used and with the data analysis. Our findings suggest that DNA sequence preferences have only small effects on the positioning of individual nucleosomes throughout the genome in vivo. |
| Rights: | © The Author(s) 2009. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. | | http://creativecommons.org/licenses/by-nc/2.5/uk/ |
| Type: | article |
| URI: | http://hdl.handle.net/2115/68283 |
| Appears in Collections: | 農学院・農学研究院 (Graduate School of Agriculture / Faculty of Agriculture) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 高須賀 太一
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