They added the chemical that activated the first gene (corresponding to barcode A) for 24 hours, followed by that for the second gene (corresponding to barcode B) for the next 24 hours. “In theory, we should have enabled all uptake proteins throughout the process, but only the RNA for signal A in the first half and signal B in the second half,” says Bhattarai-Kline.
When the scientists changed the order of the E coliThat’s exactly what they found: The DNA evidence for barcode A was first integrated into the Crispr array, followed by that of barcode B. To double-check their work, they reversed the terms and added the chemical fabric for barcode B before that of A. Again the Crispr array read out the expected pattern. This indicated that the Retro-Cascorder registered the expression of both genes in the correct order.
While others recording systems have been developed That store information in DNA, the one created by Shipman’s group, has an extra degree of specificity — the gene-specific barcodes — coupled with the ability to view gene expression in sequence. “It’s a really cool demonstration and optimization of cell uptake,” said Timothy Lu, a synthetic biologist at the Massachusetts Institute of Technology who was not involved in the study.
Harris Wang, a biologist at Columbia University who has developed molecular recording systems, agrees. This work “push us into new territory in terms of how we can gather information about the inner workings of the cell,” he says, adding that “you have much better control over which signals to record.” Wang, who was not part of the study, wonders if these recording systems will ever be able to keep track of how much a gene is on or off, since gene expression doesn’t always work on a binary scale. For example, something like epigenetic regulation (chemical changes in DNA) can easily modulate genes to be expressed at different levels, rather than simply turning them on or off.
Lu is interested in seeing this system, and other cell registration systems, once implemented in mammalian cells — an interest shared by Shipman and his team. “Our long-term goal is to capture really complex events that play out for weeks and months in mammalian development and disease states,” Shipman says. Then, for something like cancer or Parkinson’s, scientists may be able to better understand how different genes are turned on and off as the disease progresses.
In the near future, the scientists see the Retro-Cascorder as an extra piece of equipment that can turn a bacterium into a biosensor. These bacteria can be released to monitor chemical exposure in wastewater or study the human gut. Bacteria “interact with their environment, and they sense a lot of things that we would normally care about on a very sensitive level,” Shipman says. “If we can just let them store that information, then we can put them to work in an environment that’s hard to control.” Because substances such as pollutants and metabolites often trigger changes in gene expression, the bacteria’s DNA receipt book can be used to identify which molecules are present when.
For now, Shipman is thankful that the Retro-Cascorder is working. It shows that cell parts can be rigged for newer purposes. “We let evolution take us to something useful, and then we choose it as the icing on the cake,” he says with a laugh.
Update 12/8/2022 at 12:11 PM: This story was updated to correct Seth Shipman’s primary connection.
