Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements

Byungjin Hwang, Wookjae Lee, Soo-Young Yum, Yujin Jeon, Namjin Cho, Goo Jang () and Duhee Bang ()
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Byungjin Hwang: Yonsei University
Wookjae Lee: Yonsei University
Soo-Young Yum: Seoul National University
Yujin Jeon: Yonsei University
Namjin Cho: Yonsei University
Goo Jang: Seoul National University
Duhee Bang: Yonsei University

Nature Communications, 2019, vol. 10, issue 1, 1-9

Abstract: Abstract Determining cell lineage and function is critical to understanding human physiology and pathology. Although advances in lineage tracing methods provide new insight into cell fate, defining cellular diversity at the mammalian level remains a challenge. Here, we develop a genome editing strategy using a cytidine deaminase fused with nickase Cas9 (nCas9) to specifically target endogenous interspersed repeat regions in mammalian cells. The resulting mutation patterns serve as a genetic barcode, which is induced by targeted mutagenesis with single-guide RNA (sgRNA), leveraging substitution events, and subsequent read out by a single primer pair. By analyzing interspersed mutation signatures, we show the accurate reconstruction of cell lineage using both bulk cell and single-cell data. We envision that our genetic barcode system will enable fine-resolution mapping of organismal development in healthy and diseased mammalian states.

Date: 2019
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DOI: 10.1038/s41467-019-09203-z

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