In vivo generation of DNA sequence diversity for cellular barcoding

Nucleic Acids Res. 2014;42(16):e127. doi: 10.1093/nar/gku604. Epub 2014 Jul 10.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Shuffling
  • Escherichia coli / genetics
  • Genetic Variation
  • High-Throughput Nucleotide Sequencing / methods*
  • Integrases
  • Recombinases
  • Sequence Analysis, DNA / methods*


  • Recombinases
  • Cre recombinase
  • Integrases