Weber, Tom S. and Dukes, Mark and Miles, Denise C. and Glaser, Stefan P. and Naik, Shalin H. and Duffy, Ken R. (2016) Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system. BMC Systems Biology, 10 (43). ISSN 1752-0509

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Abstract

Background Cellular barcoding is a recently developed biotechnology tool that enables the familial identification of progeny of individual cells in vivo. In immunology, it has been used to track the burst-sizes of multiple distinct responding T cells over several adaptive immune responses. In the study of hematopoiesis, it revealed fate heterogeneity amongst phenotypically identical multipotent cells. Most existing approaches rely on ex vivo viral transduction of cells with barcodes followed by adoptive transfer into an animal, which works well for some systems, but precludes barcoding cells in their native environment such as those inside solid tissues. Results With a view to overcoming this limitation, we propose a new design for a genetic barcoding construct based on the Cre Lox system that induces randomly created stable barcodes in cells in situ by exploiting inherent sequence distance constraints during site-specific recombination. We identify the cassette whose provably maximal code diversity is several orders of magnitude higher than what is attainable with previously considered Cre Lox barcoding approaches, exceeding the number of lymphocytes or hematopoietic progenitor cells in mice. Conclusions Its high diversity and in situ applicability, make the proposed Cre Lox based tagging system suitable for whole tissue or even whole animal barcoding. Moreover, it can be built using established technology.

Item Type:	Article
Keywords:	Cell fate tracking; Cellular barcoding; Cre lox system; DNA stochastic programme; Combinatorial explosion;
Academic Unit:	Faculty of Science and Engineering > Research Institutes > Hamilton Institute
Item ID:	8187
Identification Number:	https://doi.org/10.1186/s12918-016-0290-3
Depositing User:	Dr Ken Duffy
Date Deposited:	03 May 2017 11:31
Journal or Publication Title:	BMC Systems Biology
Publisher:	BioMed Central
Refereed:	Yes
URI:	Publisher
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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