Recording device for the cell history

Different "events" such as virus infections, as well as exposure to environmental toxins or other forms of stress, alter the activity of genes, leaving molecular traces in the body. Inside the cell. These changes occur mainly at the level of messenger RNA (mRNA). These are molecules that encode genetic information when genes are activated and read, a process known as transcription. Researchers can accurately study the activity of a gene by measuring the molecules of mRNA present in a cell. However, traces of gene transcription disappear rapidly: mRNA is highly unstable and cells often degrade it after a short time.

Randall Platt, a researcher at ETH, and his colleagues at the Department of Biosystems Science and Engineering have developed a molecular recording system that records transcription events in DNA, where they can be stored permanently, then sequenced.

To create their "recording device", Platt PhD students Florian Schmidt and Mariia Cherepkova used the CRISPR-Cas system. CRIPSR-Cas is an adaptive immune system for bacteria and archaea. The system functions as an immunological memory device by recording genetic information on pathogens infecting the cell. This genetic information is recorded in a specific part of the DNA called the CRISPR matrix – a process called acquisition.

CRISPR matrices are capable of storing short DNA sequences, called "spacers", derived from a pathogen. The spacers are separated from each other by a short identical DNA sequence called direct repeat, just like the beads of a chain.

The researchers worked with the intestinal bacterium Escherichia coli, introducing the CRISPR-Cas system genes from a different bacterial species. One of these genes Cas is fused to a reverse transcriptase, an enzyme that uses an RNA molecule to produce a DNA encoding the same information. In other words, he transcribes the RNA into DNA.

Escherichia coli cells with foreign genes for this CRISPR-Cas were able to produce a protein complex that binds to short mRNA molecules. Reverse transcriptase translates these RNA spacers into DNA, containing the same information as the original RNA, and then stores them in the CRISPR matrix. This process can occur multiple times, so that new spacers are added to the CRISPR array in the reverse chronological order, so that the last acquired DNA fragment is always the first.

In principle, this allows you to save any number of spacers in a CRISPR table. Since DNA is very stable, the information it contains is stored for a long time and is also passed from one generation to the next.

"Our system is a biological data logger that records the genetic response of bacteria to external influences and allows us to access this information even after many bacterial generations," said Florian Schmidt, lead author of the report. study, recently published in the journal. Nature.

According to Professor Randall Platt of ETH, "researchers have long been working on the creation of synthetic cellular memory forms, but we are the first to develop one that can record information about the expression of each gene in a cell over time ". The researchers worked more than two years on this system.

Until now, researchers were limited to measuring mRNA in a single snapshot over time. Taking these snapshots usually means destroying the cell, extracting its mRNA, and then quantifying them. In contrast, the new CRISPR-Cas RNA recording system records the history of the cell, allowing researchers to effectively access the entire cellular logbook rather than a single instant.

As part of their study, researchers at ETH recorded the reaction of E. coli bacteria equipped with the data logger with paraquat herbicide. This substance causes changes in the transcription of mRNA in cells, and scientists could read this response from the CRISPR charts even a few days after exposure to the herbicide. Without the data logger, any molecular trace of the bacteria's contact with the herbicide would have long been broken down and the information lost.

Such biological data loggers, in addition to being of interest for research purposes, could also be used as a kind of sensor, for measuring environmental toxins such as herbicide or for diagnosis. This study intriguingly demonstrates the feasibility of such an approach, but practical applications are still far away. The Randall Platt research team in Basel is already working on the transfer of the system to other cell types and paves the way for its effective use as a diagnostic tool.

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