They added the chemical that triggered the first gene (corresponding to barcode A) for 24 hours, followed by the chemical for the second gene (corresponding to barcode B) for the next 24 hours. “In theory, we should turn on all recording 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 sequenced the E. coli, they found just that: the DNA evidence for barcode A was integrated into the Crispr array first, followed by that of barcode B. To verify their work, they reversed the conditions and added the chemical for barcode B before that from A. Once again, the Crispr array read out the expected pattern. This showed that the retro-cascorder recorded the expression of both genes in the correct order.
While other recording systems have been developed that store information in DNA, the one Shipman’s group produced has an additional level of specificity – the gene-specific barcodes – coupled with the ability to sequence gene expression. “It’s a really cool demonstration and optimization of cell recording,” says Timothy Lu, a synthetic biologist at Massachusetts Institute of Technology who was not involved with the study.
Harris Wang, a biologist at Columbia University who has developed molecular recording systems, agrees. This work “pushes 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 what signals you can record.” Wang, who was not involved in the study, is excited to see if one day these recording systems will be able to track the degree to which a gene is turned on or off, since gene expression doesn’t always operate on a binary scale. For example, something like epigenetic regulation (chemical changes to DNA) can modulate genes to be expressed at different levels, rather than simply turning them on or off.
Lu is interested in seeing how this system and other cell-recording systems will one day be implemented in mammalian cells — an interest Shipman and his team share. “Our long-term goal is to record really complex events that play out over weeks and months in mammalian development and disease states,” says Shipman. Then, with something like cancer or Parkinson’s, scientists could better understand how different genes are turned on and off over the course of the disease.
In the near future, scientists envision the retro-cascorder as an additional device that could turn a bacterium into a biosensor. These bacteria could be released to track chemical loads in wastewater or study the human gut. Bacteria “interact with their environment and perceive many things that would normally interest us on a very sensitive level,” says Shipman. “If we could only get them to store this information, we could use them in an environment that is difficult to monitor.” Because substances such as pollutants and metabolites often cause changes in gene expression, the DNA recipe book of the bacterium determine which molecules are present and when.
For now, Shipman is grateful that the retro cascorder works. It shows that cell parts can be jerry-rigged for newer purposes. “We let evolution lead us to something useful and then choose it,” he says, laughing.