1974–1981 Nucleic Acids Research, 2006, Vol. 34, No. 7 doi:10.1093/nar/gkl078 Aspects of large-scale chromatin structures in mouse liver nuclei can be predicted from the DNA sequence Alfred Cioffi, Tomara J. Fleury and Arnold Stein* Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA Received November 1, 2005; Revised November 23, 2005; Accepted March 3, 2006 ABSTRACT The large amount of non-coding DNA present in mammalian genomes suggests that some of it may play a structural or functional role. We provide evidence that it is possible to predict computa- tionally, from the DNA sequence, loci in mouse liver nuclei that possess distinctive nucleosome arrays. We tested the hypothesis that a 100 kb region of DNA possessing a strong, in-phase, dinucleosome period oscillation in the motif period-10 non-T, A/T, G, should generate a nucleosome array with a nucleo- some repeat that is one-half of the dinucleosome oscillation period value, as computed by Fourier anal- ysis of the sequence. Ten loci with short repeats, that would be readily distinguishable from the pervasive bulk repeat, were predicted computationally and then tested experimentally. We estimated experi- mentally that less than 20% of the chromatin in mouse liver nuclei has a nucleosome repeat length that is 15 bp, or more, shorter than the bulk repeat value of 195 ± bp. All 10 computational predictions were confirmed experimentally with high statistical significance. Nucleosome repeats as short as 172 ± 5 bp were observed for the first time in mouse liver chromatin. These findings may be useful for identify- ing distinctive chromatin structures computationally from the DNA sequence. INTRODUCTION One well-studied aspect of chromatin structure is nucleosome positioning. Nucleosome positioning is of interest because it is widespread in yeast (1), and it could, in principle, serve to control the accessibility of regulatory protein binding sites in all eukaryotes. However, the extent of nucleosome positioning in vivo that occurs as a direct consequence of histone-DNA interactions and the mechanisms involved in positioning are not clear. Some regions of DNA can exclude nucleosomes either because they bind to other proteins (2) or because they contain sequences that discourage nucleosome formation (3–5). In either case, the excluded region could then provide a boundary that serves to position adjacent nucleosomes (6). Additionally, both natural and synthetic sequences have been found that possess the ability to position nucleosomes directly through histone-DNA interactions; a variety of DNA sequence motifs have been implicated in nucleosome positioning (7,8). In addition to the ability of a DNA sequence to control the access of a binding site in its immediate vicinity for a regulatory protein through nucleosome positioning, sequence motifs in genomic DNA, particularly in metazoans, might be involved in other aspects of chromatin structure. For example, a periodic motif in DNA that persists over a large distance might inﬂuence nucleosome array formation. For this role, nucleosome positioning need not be precise. It is likely that nucleosome arrays that possess differences in the regularity of nucleosome spacing or differences in the nucleosome repeat length also possess differences in chromatin higher-order structure (9,10), or at least in chromatin ﬁber ﬂexibility (11). Moreover, these physical chemical differences could be functionally important. With the sequences of human, mouse and other higher organism genomes now available, one can analyze large amounts of sequence computationally and possibly obtain useful information about chromatin struc- ture if one knows what to look for. A goal for the future of genome research is to identify the structural and functional components encoded, perhaps in unexpected ways, in the large amounts of non-coding DNA that is present (12). Little is known about information in DNA that could affect large-scale chromatin structures. We have previously found that regular oscillations of period-10 non-T, A/T, G (VWG), a periodic motif that is very abundant in vertebrate genomes (13), occurred speciﬁc- ally in regions of DNA that ordered nucleosomes into regular arrays in vitro (14). The period of these oscillations, assessed *To whom correspondence should be addressed. Tel: +1 765 494 6546; Fax: +1 765 494 0876; Email: astein@bilbo.bio.purdue.edu The Author 2006. 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@oxfordjournals.org