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

3D genomics mainly focuses on the 3D position of single genes at cell level, while spatial genomics focuses more on tissue level. In this exciting new era of 3D/spatial genomics,, half-century old FISH and its derivative methods, including Tn5-FISH, play important role. 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 structure 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 kilobase level, Tn5-FISH holds great potential to detect chromosomal structures in a high-throughput manner, thus bring the dawn for the new discoveries in the great era of 3D/spatial genomics.