Zhang Xu
Li Guipeng
Yan Pixi
Yan Qing
Dai Qionghai
Jin Dayong
Shen Xiaohua
Wang Jichang
Zhang Michael Q.
Gao Juntao
1School of Medicine, Tsinghua University, Beijing 100084, China
2Department of Automation, Tsinghua University, Beijing 100084, China
3Beijing Institute of Collaborative Innovation, Beijing 100094, China
4Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
5Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
6MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist; Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
7Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, NSW 2007, Australia.
8UTS-SUStech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
9Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
10Department of histology and embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
11Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas, TX 75080-3021, USA
More InformationCorresponding author: E-mail address: jtgao@tsinghua.edu.cn (Gao Juntao)
Publish Date:2020-12-25
Abstract
Abstract
There is an increasing interest in understanding how three-dimensional (3D) organization of the genome is regulated. Different strategies have been employed to identify genome-wide chromatin interactions. However, due to current limitations in resolving genomic contacts, visualization and validation of these genomic loci with sub-kilobase resolution remain unsolved to date. Here, we describe Tn5 transposase-based Fluorescencein situhybridization (Tn5-FISH), a PCR-based, cost-effective imaging method, which can co-localize the genomic loci with sub-kilobase resolution, dissect genome architecture, and verify chromatin interactions detected by chromatin configuration capture (3C)-derived methods. To validate this method, short-range interactions in keratin-encoding gene (KRT) locus in topologically associated domain (TAD) 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 the clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.Keywords: Chromatin interaction,
Cellular imaging,
Super resolution
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