Author: Soh Ishiguro 1, Kana Ishida 2, Rina C. Sakata 1, Minori Ichiraku 3, Ren Takimoto 1, Rina Yogo 1, Yusuke Kijima 1, Hideto Mori 4, Mamoru Tanaka 5, Samuel King 1, Shoko Tarumoto 6, Taro Tsujimura 6, Omar Bashth 1, Nanami Masuyama 1,7,8, Arman Adel 1, Hiromi Toyoshima 5, Motoaki Seki 5, Ju Hee Oh 1, Anne-Sophie Archambault 1, Keiji Nishida 9,10, Akihiko Kondo 1,9,10,11, Satoru Kuhara 12, Hiroyuki Aburatani 5, Ramon I. Klein Geltink 1, Takuya Yamamoto 3,6, Nika Shakiba 1,4, Yasuhiro Takashima 3 & Nozomu Yachie 1,4,5
DOI: 10.1038/s41587-025-02649-1
1. School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia
2. Spiber Inc.
3. Center for iPS Cell Research and Application, Kyoto University
4. Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), The University of Osaka
5. Research Center for Advanced Science and Technology, The University of Tokyo
6. Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University
7. Institute for Advanced Biosciences, Keio University
8. Systems Biology Program, Graduate School of Media and Governance, Keio University
9. Engineering Biology Research Center, Kobe University
10. Graduate School of Science, Technology and Innovation, Kobe University
11. Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University
12. Graduate School of Bioresource and Bioenvironmental Sciences Faculty of Agriculture, Kyushu University
Abstract
Cell-tagging strategies with DNA barcodes have enabled the analysis of clone size dynamics and clone-restricted transcriptomic landscapes in heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here we present a multi-kingdom genetic barcoding system, CloneSelect, which enables a target cell clone to be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first stably tagged with DNA barcodes and propagated so that their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored during the experiment using CRISPR base editing. CloneSelect is scalable and compatible with single-cell RNA sequencing. We demonstrate the versatility of CloneSelect in human embryonic kidney 293T cells, mouse embryonic stem cells, human pluripotent stem cells, yeast cells and bacterial cells.
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