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Nucleic Acids Research 2005 33(3):934-945; doi:10.1093/nar/gki224
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Published online 16 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation

Yamini Dalal, Tomara J. Fleury, Alfred Cioffi and Arnold Stein*

Department of Biological Sciences, Purdue University West Lafayette, IN 47907, USA

*To whom correspondence should be addressed. Tel: +1 765 494 6546; Fax: +1 765 494 0876; Email: astein{at}bilbo.bio.purdue.edu

Received December 7, 2004. Revised January 14, 2005. Accepted January 14, 2005.

We have experimentally examined the characteristics of nucleosome array formation in different regions of mouse liver chromatin, and have computationally analyzed the corresponding genomic DNA sequences. We have shown that the mouse adenosine deaminase (MADA) gene locus is packaged into an exceptionally regular nucleosome array with a shortened repeat, consistent with our computational prediction based on the DNA sequence. A survey of the mouse genome indicates that <10% of 70 kb windows possess a nucleosome-ordering signal, consisting of regular long-range oscillations in the period-10 triplet motif non-T, A/T, G (VWG), which is as strong as the signal in the MADA locus. A strong signal in the center of this locus, confirmed by in vitro chromatin assembly experiments, appears to cooperate with weaker, in-phase signals throughout the locus. In contrast, the mouse odorant receptor (MOR) locus, which lacks locus-wide signals, was representative of ~40% of the mouse genomic DNA surveyed. Within this locus, nucleosome arrays were similar to those of bulk chromatin. Genomic DNA sequences which were computationally similar to MADA or MOR resulted in MADA- or MOR-like nucleosome ladders experimentally. Overall, we provide evidence that computationally predictable information in the DNA sequence may affect nucleosome array formation in animal tissue.

Present address: Yamini Dalal, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA


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