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用于评估DNA核小体排除序列及与结合因子结合能力的NXSensor网络工具。

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

作者信息

Luykx Peter, Bajić Ivan V, Khuri Sawsan

机构信息

Department of Biology, University of Miami, Coral Gables, FL 33124, USA.

出版信息

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W560-5. doi: 10.1093/nar/gkl158.

DOI:10.1093/nar/gkl158
PMID:16845070
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1538820/
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.

摘要

核小体作为真核染色质的基本结构单元，在调节基因表达方面发挥着重要作用。我们基于经验和理论研究中已知的DNA序列开发了一种网络工具，以影响DNA弯曲和灵活性，并排除核小体。NXSensor（可在http://www.sfu.ca/~ibajic/NXSensor/获取）可找到核小体排除序列，评估其长度和间距，并计算出一个“可及性得分”，该得分给出了可能无核小体的碱基对比例。将NXSensor应用于管家（HK）基因和组织特异性（TS）基因的启动子区域，发现这两类基因之间存在显著差异，前者平均而言明显更开放，尤其是在转录起始位点（TSS）附近。NXSensor在评估参与基因调控和染色质功能其他方面的区域中核小体形成的可能性方面应是一个有用的工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec5d/1538820/fcfe9eb046b0/gkl158f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec5d/1538820/aa229319e192/gkl158f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec5d/1538820/3b632694b87c/gkl158f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec5d/1538820/fcfe9eb046b0/gkl158f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec5d/1538820/aa229319e192/gkl158f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec5d/1538820/3b632694b87c/gkl158f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec5d/1538820/fcfe9eb046b0/gkl158f3.jpg

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Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions.在缺乏Spt6介导的启动子区域染色质重新组装的情况下，转录激活因子对于转录是可有可无的。
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