Jenjaroenpun Piroon, Chew Chee Siang, Yong Tai Pang, Choowongkomon Kiattawee, Thammasorn Wimada, Kuznetsov Vladimir A
Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 138671, Singapore Interdisciplinary Graduate Program in Genetic Engineering, Graduate School, Kasetsart University, Bangkean, Bangkok 10900, Thailand.
Open source Computing and Technology Innovation, Bioinformatics Institute, 138671, Singapore.
Nucleic Acids Res. 2015 Jan;43(Database issue):D110-6. doi: 10.1093/nar/gku970. Epub 2014 Oct 16.
A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser.
三链体靶DNA位点（TTS）是一段由多聚嘌呤组成的DNA，它能够与三链体形成寡核苷酸（TFO）形成三链体（三螺旋）结构，并能够影响基因表达的位点特异性调控和/或基因组DNA的修饰。基因组TTS与基因调控信号和功能基因组结构的共定位表明，TFOs有可能被用于癌症和其他遗传疾病治疗的反基因策略中。在此，我们展示了TTS定位与整合（TTSMI；http://ttsmi.bii.a-star.edu.sg）数据库，该数据库提供了人类基因组中独特TTS位置的目录，以及用于分析TTS与基因组调控序列和信号共定位的工具，这些调控序列和信号是使用下一代测序技术鉴定出来的和/或通过计算模型预测的。TTSMI被设计成一个用户友好的工具，它有助于（i）使用与序列稳定性和特异性相关的几个搜索词和标准快速搜索/筛选TTS，（ii）对与基因调控信号和非B DNA结构共定位的TTS进行交互式筛选，（iii）探索特定TTS生物信号的动态组合，以及（iv）通过UCSC基因组浏览器同时将一个TTS与各种注释轨迹进行可视化展示。
