MaMemories can live on in the brain as very compelling material. This is the definition of the word “engram”, which describes the physical content of how memories are stored. But memories extend beyond the organism level. Cells also hold memories of the different genes that are expressed over time. Cis-regulatory elements (CREs) control gene expression, so measuring the activity of these CREs can provide insight into how genes are expressed in cells. However, Existing Technology It is only possible to record the gene regulation of a cell at a specific point in time.1
We sought to find a way to document the activities of these CREs over time. Jay ShendureA geneticist at the University of Washington and his team developed a technique called Enhancer-Driven Genomic Multiplexed Recording of Transcriptional Activity (ENGRAM).2 By using prime editing, which allows short, unique DNA sequences to be inserted into specific locations, Shendur and his team were able to track and write gene regulatory information into locations across the genome. Nature, This could provide insight into how specific genes shape cell identity over time.2
CREs are DNA regions that control the expression of nearby genes. Just before a gene is turned on, a transcription factor binds to a part of the CRE, initiating the process of gene expression. In the ENGRAM system, the team used a CRE to drive a prime-editing guide RNA (pegRNA) to insert a small DNA sequence (a barcode) into a specific location in the genome. When a CRE is turned on, it makes a prime edit and writes the corresponding barcode. By assigning a unique barcode to each CRE, scientists can track the activity of different CREs.
By using the same spacer sequence for each PEG-RNA, the scientists ensured that all the barcodes were written into the same place in the genome, creating a “list” of barcodes. “That’s the key to multiplexing,” they say. Wei Chenis a co-author on the paper and was previously a graduate student in Shendur’s lab. Chen is now a postdoctoral researcher at the Institute for Protein Design.
The scientists were able to sequence the cells’ DNA to see which barcodes had been written, revealing the cell’s regulatory history. When the scientists tested the system in living cells to see if the number of barcodes recorded matched the amount of RNA produced by gene expression, they found that the two correlated with each other, demonstrating that CREs provide a quantitative view of the extent of expression.
Next, the scientists tested whether the ENGRAM recorder system could properly capture the effects of multiple signals by incorporating three CREs that activate in response to different stimuli, such as drug administration. They found that the recorded barcodes reflected the amount of external signal applied – for example, more signal resulted in more barcodes.
Finally, the team tested ENGRAM in mouse embryonic cells, where they were able to measure the activity of 98 synthetic CREs as the cells differentiated over time. “Ultimately, we can map the dynamics of different signals over time,” Chen said.
“[The study] “This addresses a key limitation in the field, which is the need for the ability to record expression levels directly from genes.” Harris Wangis a biologist at Columbia University who was not involved in the study.
Some may worry that the process of inserting synthetic DNA into a genome to record the activity of regulatory elements might itself disrupt the normal state of the cell. Reza KalholJonathan Myers, a bioengineer at Johns Hopkins University who was not involved in the study, says it’s an unavoidable risk. “The Heisenberg principle says you can’t measure something without changing it,” he says.
For Shendure, it’s about uncovering the cell’s journey, not just seeing the final destination: “Our vision is to get to a world where we can routinely make measurements across every cell in a system that reflect not just the final dynamics of the system, but everything that happened along the way,” he said.
