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Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system
- Source :
- BMC Systems Biology
- Publication Year :
- 2016
- Publisher :
- BioMed Central, 2016.
-
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. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0290-3) contains supplementary material, which is available to authorized users.
- Subjects :
- QA75
0301 basic medicine
In situ
Distance constraints
Code diversity
Computational biology
CD8-Positive T-Lymphocytes
Biology
Quantitative Biology - Quantitative Methods
DNA barcoding
Mice
03 medical and health sciences
Structural Biology
Modelling and Simulation
Cell Behavior (q-bio.CB)
Animals
Molecular Biology
Quantitative Methods (q-bio.QM)
Recombination, Genetic
Integrases
Applied Mathematics
Inverted Repeat Sequences
Genetic Variation
DNA stochastic programme
3. Good health
Computer Science Applications
Cre lox system
030104 developmental biology
FOS: Biological sciences
Modeling and Simulation
Cellular barcoding
Quantitative Biology - Cell Behavior
Hematopoietic progenitor cells
Cre-Lox recombination
Genetic Engineering
Combinatorial explosion
Cell fate tracking
Ex vivo
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 17520509
- Database :
- OpenAIRE
- Journal :
- BMC Systems Biology
- Accession number :
- edsair.doi.dedup.....ad428fcb4a97e9536b509ad449615010