Scientists are constructing a DNA recipe book to store the history of cells

Gladstone scientists are developing living biosensors to track the genetic activity of cells

SAN FRANCISCO, July 27, 2022 /PRNewswire/ — If you want to track someone’s activity for a day, you can call them every ten minutes and ask what they’re doing. However, it would be easier to provide them with a diary to log their own actions. Scientists often rely on a method similar to the first to track how cells change over time; They pick cells from a group at fixed times and take a snapshot of their genetic activity.

Researchers at Gladstone developed a biological device called a retro-cascorder that logs a cell’s genetic activity for days by recording data in strands of DNA. Photo: Michael Short/Gladstone Institutes

Now researchers at the Gladstone Institutes have developed a tool that’s more like a diary or receipt book — it records a cell’s genetic activity for days. Dubbed the retro-cascorder, the biological device records data in strands of DNA, which can then be analyzed at any time to obtain the cell’s activity log.

“This new way of capturing molecular data gives us an unprecedented window into cells,” says Gladstone Assistant Investigator Seth ShipmanPhD, senior author of the new study published in the journal Nature. “Besides providing a new tool for basic research, it allows us to engineer cells into living biosensors that can record changes in their environment.”

A new toolbox

While all cells within an organism have identical genomes, they differ in which genes are turned on or off at any given time. Researchers can measure the degree to which a particular gene is activated within a cell at different times to track how the cell’s behavior, function or identity changes over time.

Shipman and his colleagues wanted to develop a system that would automatically record each time a specific gene was turned on. This would allow a more detailed look at a gene’s activity pattern. Shipman has long been interested in using DNA to store data – in 2017 he encoded a movie in the DNA of living bacteria – so DNA was a natural medium for the cellular logbook.

“DNA is a flexible data storage medium that you can really encode whatever you want into,” says Shipman. “It’s also easy to use because it’s already in cells.”

For the first step in developing the retro-cascorder, Shipman’s group turned to retrons, bacterial elements that produce a specific DNA sequence when activated. The researchers added a retron to the gene of interest. Each time the gene was activated, the Retron machinery also generated a corresponding piece of DNA with a barcode unique to that gene.

“This retron acts like a receipt, telling you the gene has just been turned on,” he says Santi Bhattarai Klinethe first author of the new paper and a former research associate at Gladstone.

Next, the team wanted a molecular ledger to record this evidence in chronological order. To do this, they used CRISPR arrays, long, repeating DNA sequences into which bacteria normally copy parts of the genetic information they need for immune memory – in the order in which they receive this information.

By integrating these arrays into the same cells as the retron machinery, Shipman’s group ensured that every DNA recipe produced by the retrons was inserted into the CRISPR array. To retrieve the information contained in the CRISPR array, the researchers simply had to sequence the cell’s genome and look at the sequence of retron receptions in the array.

Cellular Sensors

To demonstrate the usefulness of their new retro cascorder, Shipman and his colleagues constructed Escherichia coli (E. coli) Cells that contain retrons in genes that are known to be activated in the presence of certain chemicals. They showed that over 48 hours, a CRISPR array could accurately record the order in which those genes were turned on — and thus the order in which the researchers added those chemicals.

“We think our system will be most useful in the short term for this type of application,” says Bhattarai-Kline. ‘Researchers could install multiple biosensors in a cell and use them to monitor an environment over time, from a pond or a sewage treatment plant to the inside of the human gut.’

In its current form, the retro-cascorder only tells researchers the order in which genes were turned on, not the time that elapsed between those events. However, CRISPR arrays are constantly adding small pieces of free-floating DNA to cells as part of their immune memory function. If researchers discover that they’re added at a predictable pace, these DNA bits could provide a sort of molecular clock that tells exactly when each retron is integrated, and thus when each gene is activated.

So far, Shipman’s group has only used the system to track a few genes at a time, rather than the many dozens researchers might want to simultaneously monitor in the future. However, the team is actively working on ways to extend Retro-Cascorder and adapt the system for use in cell types other than bacteria.

“It’s not a perfect system yet, but we think it will still be better than existing methods that only allow you to measure one event at a time,” says Shipman.

About the research project

The paper “Recording gene expression order in DNA by CRISPR addition of retron barcodes” was published in the journal Nature on July 27, 2022.

Other authors are Sierra Lears, Chloe Fischmanand Santiago Lopez by Gladstone; Elana Lockschin from Duke University; Maxim Schubert and George Church from Harvard University; and Jeff Nivala of University of Washington.

Work was supported by the Simons Foundation Autism Research Initiative, Pew Biomedical Scholars Program, National Institute of General Medical Sciences (1DP2GM140917-01), UCSF Program for Breakthrough Biomedical Research, LK Whittier Foundation, National Science Foundation (2034836) and a Berkeley Fellowship for Graduate Study.

About Gladstone Institute

To ensure our work delivers the greatest benefit, the Gladstone Institutes focus on diseases with profound medical, economic and social implications – unsolved diseases. Gladstone is an independent, not-for-profit life sciences research organization that uses visionary science and technology to overcome disease. It has an academic connection with the University of California, San Francisco.

Media contact: Julie Langeler | Deputy Director, Communications | | 415.734.5000
1650 Owens Street, San Francisco, CA 94158 |

Gladstone Institute logo (PRNewsphoto/Gladstone Institutes)

Gladstone Institute logo (PRNewsphoto/Gladstone Institutes)



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