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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Luykx P,Bajić IV,Khuri Sdoi
10.1093/nar/gkl158subject
Has Abstractpub_date
2006-07-01 00:00:00pages
W560-5issue
Web Server issueeissn
0305-1048issn
1362-4962pii
34/suppl_2/W560journal_volume
34pub_type
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