In vivo generation of DNA sequence diversity for cellular barcoding

Nucleic Acids Research
Ian D PeikonAnthony M Zador

Abstract

Heterogeneity is a ubiquitous feature of biological systems. A complete understanding of such systems requires a method for uniquely identifying and tracking individual components and their interactions with each other. We have developed a novel method of uniquely tagging individual cells in vivo with a genetic 'barcode' that can be recovered by DNA sequencing. Our method is a two-component system comprised of a genetic barcode cassette whose fragments are shuffled by Rci, a site-specific DNA invertase. The system is highly scalable, with the potential to generate theoretical diversities in the billions. We demonstrate the feasibility of this technique in Escherichia coli. Currently, this method could be employed to track the dynamics of populations of microbes through various bottlenecks. Advances of this method should prove useful in tracking interactions of cells within a network, and/or heterogeneity within complex biological samples.

References

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Citations

May 27, 2015·Scientific Reports·Kosuke FujishimaLynn J Rothschild
Jul 2, 2016·BMC Systems Biology·Tom S WeberKen R Duffy
Dec 6, 2016·Nature Methods·Reza KalhorGeorge M Church
Mar 4, 2017·Scientific Reports·Lars ThieleckeKerstin Cornils
Nov 9, 2017·Frontiers in Computational Neuroscience·Young-Gyu YoonEdward S Boyden
Nov 1, 2018·Nature Methods·Justus M Kebschull, Anthony M Zador
Nov 30, 2019·Bioinformatics·Lars ThieleckeIngmar Glauche
Apr 28, 2017·Nucleic Acids Research·Ian D PeikonAnthony M Zador
May 22, 2019·Nature Protocols·Weike PeiHans-Reimer Rodewald
Aug 12, 2020·Annual Review of Biomedical Data Science· Sagar, Dominic Grün
Aug 11, 2018·Science·Reza KalhorGeorge M Church
Jun 30, 2019·Development·Aaron McKenna, James A Gagnon
Feb 26, 2020·Nature Ecology & Evolution·Weronika JasinskaShimon Bershtein
Oct 20, 2020·Frontiers in Physiology·Irene Garcia-GonzalezRui Benedito

Datasets Mentioned

BETA
EU935740

Methods Mentioned

BETA
PCR
dissection

Related Concepts

Cre recombinase, Enterobacteria phage P1
Alkalescens-Dispar Group
Variation (Genetics)
Sequence Determinations, DNA
Integrase
Exon Shuffling, In Vitro
Resolvases
High-Throughput Nucleotide Sequencing
DNA
Escherichia coli

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