title: NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors.
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.
authors.affiliation: Department of Biology, University of Miami, Coral Gables, FL 33124, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Luykx
authors.forename: Ivan V
authors.initials: IV
authors.lastname: Bajić
authors.forename: Sawsan
authors.initials: S
authors.lastname: Khuri
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000378:metabolism*; D020407:Internet; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D004268:DNA-Binding Proteins; D009707:Nucleosomes; D014157:Transcription Factors; D004247:DNA