Tn5-FISH,a novel cytogenetic method to image chromatin interactions with sub-kilobase resolution |
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| Institution: | 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;1. Department of Laboratory Animal Science, College of Basic Medical Science, Army Medical University, Chongqing 400038, China;2. College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China;3. National Clinical Research Center for Otolaryngologic Diseases, Beijing 100853, China;1. Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China;2. Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, China;3. Shanghai Laboratory Animal Research Center, Shanghai 201203, China;4. Institute for Digital Health, International Human Phenome Institutes (Shanghai), Shanghai 200433, China;5. Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China;6. School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China;7. Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China;8. State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China;9. Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 330106, China;1. Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia;2. Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia;3. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia;4. Pirogov Russian National Research Medical University, Research Institute of Translational Medicine, Department of Regenerative Medicine, Moscow, Russia;5. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK;6. Mental Health Research Center, Moscow, Russia;1. CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, China;2. Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China;3. University of Chinese Academy of Sciences, Beijing 100049, China;4. Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China;5. CUHK-GIBH Joint Laboratory of Stem Cell and Regenerative Medicine, Chinese University of Hong Kong, Hong Kong, China;6. Life Sciences Institute and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China;7. Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China |
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| 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. |
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| Keywords: | Chromatin interaction Cellular imaging Super resolution |
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