Different “events” such as infections by viruses, as well as the exposure to environmental toxins or other forms of stress, change the activity of genes thereby leaving molecular traces inside the cell. These changes happen mainly at the level of messenger RNA (mRNA). These are molecules that encode genetic information when genes become activated and read, a process known as transcription. Researchers can accurately investigate the activity of a gene by measuring the mRNA molecules present in a cell. However, the traces of gene transcription disappear rapidly: mRNA is highly instable, and cells often degrade it after a short time.
Circular DNA as a recording system
ETH researcher Randall Platt and his colleagues in the Department of Biosystems Science and Engineering (D-BSSE) in Basel have now developed a molecular recording system that writes transcriptional events into DNA where they can be permanently stored and later accessed to by sequencing.
To create their “recording device”, Platt’s doctoral students Florian Schmidt and Mariia Cherepkova employed the CRISPR-Cas system. CRIPSR-Cas is an adaptive immune system in bacteria and archaea. The system functions like an immunological memory device by recording genetic information about pathogens infecting the cell. This genetic information is recorded in a specific stretch of DNA known as a CRISPR array – a process called acquisition.
Genetic information like a string of pearls
CRISPR arrays are capable of storing short sequences of DNA, known as ‘spacers’, originating from a pathogen. Spacers are separated from each other by short identical DNA sequence called direct repeats, just like pearls on a string.
The researchers worked with the gut bacterium
Escherichia coli
, introducing the genes for the CRISPR-Cas system from a different bacterial species. One of those
Cas
genes is fused to a reverse transcriptase, an enzyme that uses an RNA molecule to produce DNA encoding the same information – in other words, it transcribes RNA back into DNA.
The
Escherichia coli
cells supplied with the foreign genes for this CRISPR-Cas were able to produce a protein complex that binds short mRNA molecules. The reverse transcriptase translates these RNA spacers into DNA, containing the same information as the original RNA, and subsequently storing them in the CRISPR array. This process can occur multiple times such that new spacers are added to the CRISPR array in reverse chronological order, so the most recently acquired piece of DNA is always first.
