Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Sanguinetti, Guido

IMPACT FACTOR 2018: 0.536
5-year IMPACT FACTOR: 0.764

CiteScore 2018: 0.49

SCImago Journal Rank (SJR) 2018: 0.316
Source Normalized Impact per Paper (SNIP) 2018: 0.342

Mathematical Citation Quotient (MCQ) 2018: 0.02

See all formats and pricing
More options …
Volume 7, Issue 1


Volume 10 (2011)

Volume 9 (2010)

Volume 6 (2007)

Volume 5 (2006)

Volume 4 (2005)

Volume 2 (2003)

Volume 1 (2002)

Re-Cracking the Nucleosome Positioning Code

Mark R Segal
Published Online: 2008-04-21 | DOI: https://doi.org/10.2202/1544-6115.1367

Nucleosomes, the fundamental repeating subunits of all eukaryotic chromatin, are responsible for packaging DNA into chromosomes inside the cell nucleus and controlling gene expression. While it has been well established that nucleosomes exhibit higher affinity for select DNA sequences, until recently it was unclear whether such preferences exerted a significant, genome-wide effect on nucleosome positioning in vivo. This question was seemingly and recently resolved in the affirmative: a wide-ranging series of experimental and computational analyses provided extensive evidence that the instructions for wrapping DNA around nucleosomes are contained in the DNA itself. This subsequently labeled second genetic code was based on data-driven, structural, and biophysical considerations. It was subjected to an extensive suite of validation procedures, with one conclusion being that intrinsic, genome-encoded, nucleosome organization explains approximately 50% of in vivo nucleosome positioning. Here, we revisit both the nature of the underlying sequence preferences, and the performance of the proposed code. A series of new analyses, employing spectral envelope (Fourier transform) methods for assessing key sequence periodicities, classification techniques for evaluating predictive performance, and discriminatory motif finding methods for devising alternate models, are applied. The findings from the respective analyses indicate that signature dinucleotide periodicities are absent from the bulk of the high affinity nucleosome-bound sequences, and that the predictive performance of the code is modest. We conclude that further exploration of the role of sequence-based preferences in genome-wide nucleosome positioning is warranted. This work offers a methodologic counterpart to a recent, high resolution determination of nucleosome positioning that also questions the accuracy of the proposed code and, further, provides illustrations of techniques useful in assessing sequence periodicity and predictive performance.

Keywords: motifs; periodicity; prediction; ROC curve; spectral envelope

About the article

Published Online: 2008-04-21

Citation Information: Statistical Applications in Genetics and Molecular Biology, Volume 7, Issue 1, ISSN (Online) 1544-6115, DOI: https://doi.org/10.2202/1544-6115.1367.

Export Citation

©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston.Get Permission

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

Hu Jin, H. Tomas Rube, and Jun S. Song
Nucleic Acids Research, 2016, Volume 44, Number 5, Page 2047
Paul D. Hartley and Hiten D. Madhani
Cell, 2009, Volume 137, Number 3, Page 445
Clayton K. Collings, Alfonso G. Fernandez, Chad G. Pitschka, Troy B. Hawkins, John N. Anderson, and Michael J. Pazin
PLoS ONE, 2010, Volume 5, Number 6, Page e10933
Xianfu Yi, Yu-Dong Cai, Zhisong He, WeiRen Cui, Xiangyin Kong, and Xiaoyu Zhang
PLoS ONE, 2010, Volume 5, Number 9, Page e12495
Ross M. Fraser, David Keszenman-Pereyra, Martin W. Simmen, and James Allan
Journal of Molecular Biology, 2009, Volume 390, Number 2, Page 292

Comments (0)

Please log in or register to comment.
Log in