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CRISPR used to record a film in bacteria

17 July 2017

By Lea Goetz

Appeared in BioNews 909

Scientists have used the CRISPR/Cas system to encode a film in the genomes of living bacteria.

However, the researchers' ultimate goal is not to record films or to 'put Wikipedia into bacteria', said first author Dr Seth Shipman from Harvard University to The Atlantic.

'We want to turn cells into historians,' Dr Shipman explained. 'We envision a biological memory system that's much smaller and more versatile than today's technologies, which will track many events non-intrusively over time.'

To write information into the genomes of living bacteria, the team of US scientists made use of the CRISPR/Cas 'bacterial immune system': when attacked by a virus, bacteria cut out reference snippets of viral DNA and incorporate into their genome as a reference guide for future virus attacks. Since new DNA snippets are always inserted after old ones, over its lifetime, the bacterium acquires a chronologically ordered library of viral DNA.

The researchers converted five frames from one of the world's first films, a running horse, into pixels. They encoded the tone and location of each pixel into the ATCG-letter code of DNA, forming short strands which were tagged to resemble viral DNA. They then exposed a population of Escherichia coli bacteria to the strands at a rate of one frame per day, in order to insert each frame in the correct order for the movie. The researchers could then retrieve the images by sequencing the genomes and converting back the DNA-encoded information.

The research, published in the journal Nature, demonstrated the storage and retrieval of movie frames from a bacterial population with more than 90 percent accuracy. Single images could be retrieved even after a week, corresponding to 48 bacterial generations. The work also revealed which DNA encoding scheme is most efficient and how the DNA sequence can be optimised for storage, such as by using more of the bases G and C or by placing information between so-called spacer motifs.

The team say developing cells could one day record chronological information ranging from gene expression patterns to the level of environmental pollutants. This information could be read by sequencing the cell's genome, without disturbing the system during development.

'If we had those transcriptional steps, we could potentially use them like a recipe to engineer similar cells,' said Dr Shipman. 'These could be used to model disease - or even in therapies.' The team say they hope to use the technology to study brain development.

Yet, substantial technological advances are still needed before the technique can be used reliably, and in mammalian cells, Professor Randall Platt at ETH Zurich, Switzerland, who was not involved in the study told Nature News. 'It’s full of limitations, but this is pioneering work that they’re doing.'

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