Tn5-FISH,a novel cytogenetic method to image chromatin interactions with sub-kilobase resolution  

作　　者：Jing Niu Xu Zhang Li Guipeng Pixi Yan Qing Yan Qionghai Dai Dayong Jin Xiaohua Shen Jichang Wang Michael QZhang Juntao Gao 

机构地区：[1]School of Medicine,Tsinghua University,Beijing 100084,China [2]Department of Automation,Tsinghua University,Beijing 100084,China [3]Beijing Institute of Collaborative Innovation,Beijing 100094,China [4]Medi-X Institute,SUSTech Academy for Advanced Interdisciplinary Studies,Southern University of Science and Technology,Shenzhen 518055,China [5]Department of Biology,Southern University of Science and Technology,Shenzhen 518055,China [6]MOE Key Laboratory of Bioinformatics,Bioinformatics Division,BNRist,Center for Synthetic&Systems Biology,Tsinghua University,Beijing 100084,China [7]Institute for Biomedical Materials and Devices(IBMD),Faculty of Science,University of Technology Sydney,NSW 2007,Australia [8]UTS-SUStech Joint Research Centre for Biomedical Materials and Devices,Department of Biomedical Engineering,Southern University of Science and Technology,Shenzhen 518055,China [9]Key Laboratory for Stem Cells and Tissue Engineering(Sun Yat-sen University),Ministry of Education,Guangzhou 510080,China [10]Department of histology and embryology,Zhongshan School of Medicine,Sun Yat-sen University,Guangzhou 510080,China [11]Department of Biological Sciences,Center for Systems Biology,The University of Texas,Dallas,TX 75080-3021,USA

出　　处：《Journal of Genetics and Genomics》2020年第12期727-734,共8页遗传学报（英文版）

基　　金：This work was supported in part by the State Key Research Development Program of China(2017YFA0505503);the National Natural Science Foundation of China(81890991 and 31671383);Beijing Advanced Innovation Center for Structural Bio logy,Tsinghua University(100300001);the fund from Foshan-Tsinghua Innovation Special Fund(FTISF,2019THFS0141)to J.G.,the National Natural Science Foundation of China(31871444);the program for Guangdong Introducing Innovative and Entrepreneurial Teams(2016ZT06S029)to J.W.;Australia China Science and Research Fund Joint Research Centre for POCT(ACSRF65827);Shenzhen Science and Technology Program(KQTD 20170810110913065)to D.J.

摘　　要：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.

关 键 词：Fluorescencein situhybridization Chromatin interaction Cellular imaging Super resolution 

分 类 号：R394[医药卫生—医学遗传学]