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CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria

2017; Nature Portfolio; Volume: 547; Issue: 7663 Linguagem: Inglês

10.1038/nature23017

1476-4687

Seth L. Shipman, Jeff Nivala, Jeffrey D. Macklis, George M. Church,

Gene Regulatory Network Analysis

The authors encode pixel values of a short motion picture into the DNA of a population of Escherichia coli. Among many applications, harnessing the CRISPR–Cas microbial immune system has been suggested to turn DNA into a promising medium for archiving data within living cells. Now Seth Shipman and colleagues report a quantitative leap in this direction. They have encoded a motion picture into the DNA of a population of Escherichia coli by storing pixel values as a nucleotide code inserted into the genomes of several living cells. Besides the technological feat, the work also reveals new principles in the natural functioning of the CRISPR–Cas system that are relevant for understanding the biology of bacterial adaptation as well as its practical applications. DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro1,2,3,4,5,6. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1–Cas2 integrase, the CRISPR–Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity7. When harnessed, this system has the potential to write arbitrary information into the genome8. Here we use the CRISPR–Cas system to encode the pixel values of black and white images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. We also uncover underlying principles of the CRISPR–Cas adaptation system, including sequence determinants of spacer acquisition that are relevant for understanding both the basic biology of bacterial adaptation and its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.