{"title":"(Tn5-) 3D/空间基因组学时代基于fish的成像。","authors":"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","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":"9 1","pages":"15-25"},"PeriodicalIF":0.0000,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323772/pdf/","citationCount":"0","resultStr":"{\"title\":\"(Tn5-)FISH-based imaging in the era of 3D/spatial genomics.\",\"authors\":\"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\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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.</p>\",\"PeriodicalId\":59621,\"journal\":{\"name\":\"生物物理学报:英文版\",\"volume\":\"9 1\",\"pages\":\"15-25\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2023-02-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323772/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"生物物理学报:英文版\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.52601/bpr.2023.220025\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"生物物理学报:英文版","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.52601/bpr.2023.220025","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
(Tn5-)FISH-based imaging in the era of 3D/spatial genomics.
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.