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A novel cytogenetic method to image chromatin interactions at subkilobase resolution: Tn5 transposase–based fluorescence in situ hybridization
Journal of Genetics and Genomics ( IF 5.9 ) Pub Date : 2020-11-07 , DOI: 10.1016/j.jgg.2020.04.008
Jing Niu 1 , Xu Zhang 2 , Guipeng Li 3 , Pixi Yan 1 , Qing Yan 4 , Qionghai Dai 5 , Dayong Jin 6 , Xiaohua Shen 1 , Jichang Wang 7 , Michael Q Zhang 8 , Juntao Gao 4
Affiliation  

There is an increasing interest in understanding how three-dimensional organization of the genome is regulated. Different strategies have been used to identify genome-wide chromatin interactions. However, owing to current limitations in resolving genomic contacts, visualization and validation of these genomic loci at subkilobase resolution remain unsolved to date. Here, we describe Tn5 transposase–based fluorescence in situ hybridization (Tn5-FISH), a polymerase chain reaction–based, cost-effective imaging method, which can colocalize the genomic loci at subkilobase resolution, dissect genome architecture, and verify chromatin interactions detected by chromatin configuration capture–derived methods. To validate this method, short-range interactions in the keratin-encoding gene (KRT) locus in the topologically associated domain were imaged by triple-color Tn5-FISH, indicating that Tn5-FISH is very useful to verify short-range chromatin interactions inside the contact domain and TAD. Therefore, Tn5-FISH can be a powerful molecular tool for clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.



中文翻译:

一种以亚千碱基分辨率成像染色质相互作用的新型细胞遗传学方法:基于 Tn5 转座酶的荧光原位杂交

人们对了解如何调节基因组的三维组织越来越感兴趣。已使用不同的策略来识别全基因组染色质相互作用。然而,由于目前在解析基因组接触方面的局限性,这些基因组位点在亚千碱基分辨率下的可视化和验证至今仍未解决。在这里,我们描述了基于 Tn5 转座酶的荧光原位杂交 (Tn5-FISH),这是一种基于聚合酶链反应的、具有成本效益的成像方法,它可以以亚千碱基分辨率共定位基因组位点,剖析基因组结构,并验证检测到的染色质相互作用通过染色质构型捕获衍生的方法。为了验证这种方法,角蛋白编码基因(KRT) 拓扑相关域中的位点通过三色 Tn5-FISH 成像,表明 Tn5-FISH 对验证接触域和 TAD 内的短程染色质相互作用非常有用。因此,Tn5-FISH 可以成为临床检测多种遗传疾病(如癌症)细胞遗传学变化的强大分子工具。

更新日期:2020-11-07
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