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07/20/2017

    DNA Sequencing Plays Film Chip Encoded in in Bacteria



     

    Genome engineering technology has been used to create a molecular recorder in living cells, demonstrating that genomes can be manipulated to capture and stably store practical amounts of real data. [National Institute of Mental Health]


    A team at Harvard University has used the CRISPR genome-editing tool to encode video into live bacteria. Details were reported on July 12th in the journal Nature and a trailer of sequence of images that illustrates how DNA can be encoded in—and then played back from—DNA in living cells was also released.


    “In this study, we show that two proteins of the CRISPR system, Cas1 and Cas2, that we have engineered into a molecular recording tool, together with new understanding of the sequence requirements for optimal spacers, enables a significantly scaled-up potential for acquiring memories and depositing them in the genome as information that can be provided by researchers from the outside, or that, in the future, could be formed from the cells natural experiences,“ said Church, the Robert Winthrop Professor of Genetics at Harvard Medical School and a Professor of Health Sciences and Technology at Harvard and MIT.


    The same team at led by Church built the first molecular recorder based on the CRISPR system in 2016. The recorder allows cells to acquire bits of chronologically provided, DNA-encoded information that generate a memory in a bacterium’s genome. The information is stored as an array of sequences in the CRISPR locus and can be recalled and used to reconstruct a timeline of events.


    The team used still and moving images because they represent constrained and clearly defined data sets; the movie also gave the bacteria a chance to acquire information frame by frame. “We designed strategies that essentially translate the digital information contained in each pixel of an image or frame as well as the frame number into a DNA code, that, with additional sequences, is incorporated into spacers. Each frame thus becomes a collection of spacers,” said Seth Shipman, the first author of this paper. “We then provided spacer collections for consecutive frames chronologically to a population of bacteria which, using Cas1/Cas2 activity, added them to the CRISPR arrays in their genomes. And after retrieving all arrays again from the bacterial population by DNA sequencing, we finally were able to reconstruct all frames of the galloping horse movie and the order they appeared in.”

     

    “Harnessed further, this approach could present a way to cue different types of living cells in their natural tissue environments into recording the formative changes they are undergoing into a synthetically created memory hotspot in their genomes,” said Church.


    Read more: “CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria”, Nature 547, 2017 doi:10.1038/nature23017