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

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 (availa...

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Bibliographic Details
Published in:Nucleic acids research 2006-07, Vol.34 (suppl-2), p.W560-W565
Main Authors: Luykx, Peter, Bajić, Ivan V, Khuri, Sawsan
Format: Article
Language:English
Subjects:
Binding Sites
DNA - chemistry
DNA-Binding Proteins - metabolism
Internet
Nucleic Acid Conformation
Nucleosomes - chemistry
Nucleosomes - metabolism
Promoter Regions, Genetic
Sequence Analysis, DNA - methods
Software
Transcription Factors - metabolism
User-Computer Interface
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkl158