(Tn5-)FISH-based imaging in the era of 3D/spatial genomics

Liheng Yang; Yan Yan; JunLin Li; Cheng Zhou; Jinlan Jin; Tongmei Zhang; Haokaifeng Wu; Xingang Li; Wei Wang; Li Yuan; Xu Zhang; Juntao Gao

doi:10.52601/bpr.2023.220025

Volume 9 Issue 1

Feb. 2023

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Article Navigation > Biophysics Reports > 2023 > 9(1): 15-25

Liheng Yang, Yan Yan, JunLin Li, Cheng Zhou, Jinlan Jin, Tongmei Zhang, Haokaifeng Wu, Xingang Li, Wei Wang, Li Yuan, Xu Zhang, Juntao Gao. (Tn5-)FISH-based imaging in the era of 3D/spatial genomics. Biophysics Reports, 2023, 9(1): 15-25. doi: 10.52601/bpr.2023.220025

Citation:

Liheng Yang, Yan Yan, JunLin Li, Cheng Zhou, Jinlan Jin, Tongmei Zhang, Haokaifeng Wu, Xingang Li, Wei Wang, Li Yuan, Xu Zhang, Juntao Gao. (Tn5-)FISH-based imaging in the era of 3D/spatial genomics. Biophysics Reports, 2023, 9(1): 15-25. doi: 10.52601/bpr.2023.220025

Citation:

Liheng Yang, Yan Yan, JunLin Li, Cheng Zhou, Jinlan Jin, Tongmei Zhang, Haokaifeng Wu, Xingang Li, Wei Wang, Li Yuan, Xu Zhang, Juntao Gao. (Tn5-)FISH-based imaging in the era of 3D/spatial genomics. Biophysics Reports, 2023, 9(1): 15-25. doi: 10.52601/bpr.2023.220025

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(Tn5-)FISH-based imaging in the era of 3D/spatial genomics

doi: 10.52601/bpr.2023.220025

Liheng Yang^{1, L},
Yan Yan^{2, 3, 4, L},
JunLin Li⁵,
Cheng Zhou⁶,
Jinlan Jin⁷,
Tongmei Zhang⁸,
Haokaifeng Wu^{9, 10},
Xingang Li¹³,
Wei Wang¹³,
Li Yuan^{5
,
,},
Xu Zhang^{11
,
,},
Juntao Gao^{2, 3, 4, 12
,
,}

1.
Seaver College, Pepperdine University, CA 90263, USA
2.
Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
3.
Bioinformatics Division, BNRist, Department of Automation, Beijing 100084, China
4.
MOE Key Laboratory of Bioinformatics, Beijing 100084, China
5.
Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100084, China
6.
Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
7.
Department of Critical Care Medicine, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518034, China
8.
Medical Oncology, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
9.
Centre for Regenerative Medicine and Health, HongKong Institute of Science & Innovation, Chinese Academy of Sciences, HongKong SAR, China
10.
Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, China
11.
Beijing Institute of Collaborative Innovation, Beijing 100094, China
12.
Institute for TCM-X, Beijing 100084, China
13.
Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia

More Information

Corresponding author: yuanli@gucas.ac.cn (L. Yuan); zhangx@jingjinji.cn (X. Zhang); jtgao@tsinghua.edu.cn (J. Gao)
Received Date: 30 September 2022
Accepted Date: 20 February 2023
Publish Date: 28 February 2023

Abstract

Abstract

3D genomics mainly focuses on the 3D position of single genes at the cell level, while spatial genomics focuses more on the tissue level. In this exciting new era of 3D/spatial genomics, half-century old FISH and its derivative methods, including Tn5-FISH, play important roles. In this review, we introduce the Tn5-FISH we developed recently, and present six different applications published by our collaborators and us, based on (Tn5-)FISH, which can be either general BAC clone-based FISH or Tn5-FISH. In these interesting cases, (Tn5-)FISH demonstrated its vigorous ability of targeting sub-chromosomal structures across different diseases and cell lines (leukemia, mESCs (mouse embryonic stem cells), and differentiation cell lines). Serving as an effective tool to image genomic structures at the kilobase level, Tn5-FISH holds great potential to detect chromosomal structures in a high-throughput manner, thus bringing the dawn for new discoveries in the great era of 3D/spatial genomics.
- Tn5-FISH,
- Molecular imaging,
- Chromatin interaction,
- Regulatory elements

Liheng Yang, Yan Yan, Junlin Li, Cheng Zhou, Jinlan Jin, Tongmei Zhang, Haokaifeng Wu, Xingang Li, Wei Wang, Li Yuan, Xu Zhang and Juntao Gao declare that they have no conflict of interest.
This article does not contain any studies with human or animal subjects performed by any of the authors.
Liheng Yang and Yan Yan contributed equally to this work.

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References(46)

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