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PubMed · 16845070

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

Peter Luykx·Ivan V Bajić·Sawsan Khuri
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Abstract

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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Binding SitesDNADNA-Binding ProteinsInternetNucleic Acid ConformationNucleosomesPromoter Regions, GeneticSequence Analysis, DNASoftwareTranscription FactorsUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov'tValidation Study

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Peter Luykx, Ivan V Bajić, Sawsan Khuri. 2006-07-01. NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors.. https://doi.org/10.1093/nar%2Fgkl158

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