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Nucleic Acids Research 2006 34(Web Server issue):W560-W565; doi:10.1093/nar/gkl158
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors

Peter Luykx, Ivan V. Bajic1 and Sawsan Khuri2,*

Department of Biology, University of Miami Coral Gables, FL 33124, USA 1 School of Engineering Science, Simon Fraser University Burnaby, B.C. V5A 1S6, Canada 2 The Dr. John T. Macdonald Foundation Center for Medical Genetics, University of Miami Miller School of Medicine Miami, FL 33101 USA

*To whom correspondence should be addressed. Tel: +1 305 243 6069; Fax: +1 305 243 3919; Email: skhuri{at}med.miami.edu

Received February 10, 2006. Revised March 7, 2006. Accepted March 20, 2006.

Nucleosomes, a basic structural unit of eukaryotic chromatin, play a significant role in regulating gene expression. We have developed a web tool based on DNA sequences known from empirical and theoretical studies to influence DNA bending and flexibility, and to exclude nucleosomes. NXSensor (available at http://www.sfu.ca/~ibajic/NXSensor/) finds nucleosome exclusion sequences, evaluates their length and spacing, and computes an ‘accessibility score’ giving the proportion of base pairs likely to be nucleosome-free. Application of NXSensor to the promoter regions of housekeeping (HK) genes and those of tissue-specific (TS) genes revealed a significant difference between the two classes of gene, the former being significantly more open, on average, particularly near transcription start sites (TSSs). NXSensor should be a useful tool in assessing the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.


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