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

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...

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Autores principales: Hwang, Byungjin, Lee, Wookjae, Yum, Soo-Young, Jeon, Yujin, Cho, Namjin, Jang, Goo, Bang, Duhee
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420643/
https://www.ncbi.nlm.nih.gov/pubmed/30874552
http://dx.doi.org/10.1038/s41467-019-09203-z
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author Hwang, Byungjin
Lee, Wookjae
Yum, Soo-Young
Jeon, Yujin
Cho, Namjin
Jang, Goo
Bang, Duhee
author_facet Hwang, Byungjin
Lee, Wookjae
Yum, Soo-Young
Jeon, Yujin
Cho, Namjin
Jang, Goo
Bang, Duhee
author_sort Hwang, Byungjin
collection PubMed
description 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.
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spelling pubmed-64206432019-03-18 Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements Hwang, Byungjin Lee, Wookjae Yum, Soo-Young Jeon, Yujin Cho, Namjin Jang, Goo Bang, Duhee Nat Commun Article 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. Nature Publishing Group UK 2019-03-15 /pmc/articles/PMC6420643/ /pubmed/30874552 http://dx.doi.org/10.1038/s41467-019-09203-z Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Hwang, Byungjin
Lee, Wookjae
Yum, Soo-Young
Jeon, Yujin
Cho, Namjin
Jang, Goo
Bang, Duhee
Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements
title Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements
title_full Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements
title_fullStr Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements
title_full_unstemmed Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements
title_short Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements
title_sort lineage tracing using a cas9-deaminase barcoding system targeting endogenous l1 elements
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420643/
https://www.ncbi.nlm.nih.gov/pubmed/30874552
http://dx.doi.org/10.1038/s41467-019-09203-z
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