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

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.

Graphical abstract

Keywords

Tn5-FISH / Molecular imaging / Chromatin interaction / Regulatory elements

Acknowledgements

This work was supported in part by the National Key Research and Development Program of China (2021YFE0201100, 2022YFA1103401), Beijing Municipal Natural Science Foundation (Z200021), the National Natural Science Foundation of China (81890991), CAS Interdisciplinary Innovation Team (JCTD-2020-04).

RIGHTS & PERMISSIONS

2022 The Author(s)