January 30, 2023

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Nature Chemical Biology: A new way to edit the genes of human cells!

Nature Chemical Biology: A new way to edit the genes of human cells!





Over the past decade, the CRISPR genome editing system has revolutionized molecular biology, giving scientists the ability to alter genes inside living cells for research or medical applications. Now, researchers at the Gladstone Institute have fine-tuned another efficient gene-editing system using molecules called retrons.

The research team reports in the journal Nature Chemical Biology that retrons can be optimized for efficiency and used to edit genes in a variety of cell types, from fungi to human cells .

The study is titled ” Precise genome editing across kingdoms of life using retron-derived DNA “.


Nature Chemical Biology: A new way to edit the genes of human cells!


Gladstone Associate Investigator Dr Seth Shipman , senior author of the new study, said: “This work really solidifies retrons as a platform that can be used across organisms. We can make it easier, faster and faster than current methods. Efficiently make precise modifications to genes.”

One-stop gene editing service

Most current gene-editing techniques based on the CRISPR system involve cutting out a piece of DNA from a cell’s genome and then introducing new genetic material called ” template DNA ” to replace it. When the cell repairs where the existing gene was cut, the template DNA is integrated.

This template DNA is usually produced in the laboratory and then introduced into the cell from the outside. Cas9 proteins that cleave the cell genome are delivered separately. Neither Cas9 nor template DNA can penetrate every cell, limiting the efficiency of CRISPR gene editing.

However, retrons act like DNA factories, producing abundant copies of template DNA from inside the cell. And, retrons can be delivered along with the rest of CRISPR so that cells get all the materials needed for gene editing—template DNA, Cas9, and the genetic code for molecules that help researchers track the editing process—at the same time.

“This means we only need to introduce one element per cell, ” said Santiago Lopez , first author of the new paper and a graduate student in Shipman’s lab . “This greatly simplifies the process and opens the door to new types of experiments.”

Retrofit retrons

Both Retron and CRISPR originated in bacteria; both are defense mechanisms that bacteria use to alter their DNA in response to infection. After the advent of CRISPR genome editing, the CRISPR system was chosen to selectively target genes in other cell types, and some researchers began to explore whether retrons could be used to supply templates for precise gene editing. However, the role of the different parts of the retrons structure in their function, and how these can be tuned to improve retrons, is unclear.

Shipman , an assistant professor of bioengineering and therapeutic sciences at the University of California, San Francisco (UCSF), said: “The retron system evolved to help defend against bacteria, but we wanted to change its normal function to do what we want it to do — generate genes Edit the template. “

In the new study, Shipman’s team engineered E. coli retrons to create hundreds of new variants . They tested each new variant and found a series of changes that together resulted in an 8- to 10-fold increase in the template DNA ultimately produced by retron in E. coli cells .

Next, the researchers tested the new recombinant retron system in the fungus Saccharomyces cerevisiae and in cultured human cells, and they found that the optimized system worked in all cases. This is the first demonstration of retron in human cells and its portability across cell types.

Because the team can now fine-tune exactly how much template DNA the retrons produce, they were also able to show that gene editing efficiency increases when retrons produce high levels of template DNA .

“Our study demonstrates for the first time that the more template DNA we can generate, the better the genome editing, ” Shipman said. ” Better, more precise editing ultimately means more effective and safer genomic medicine and more advanced basic research.” “

Extract tools from bacteria

Shipman says retrons are fast and useful as research tools for editing genes in different cell types in the lab. While the platform is not yet ready for use in humans, it also has the potential to help edit genes for therapeutic purposes—for example, by repairing disease-causing genetic mutations.

Since different bacteria contain different retrons, his research group also plans to explore whether other retron variants are more beneficial than the E. coli retrons they optimized in this study.

“We’re taking a general approach, mining the parts we find in bacteria and domesticating them for our own use,” Shipman said. “It’s been incredible for developing new tools, but I think We are just beginning to reap the benefits of applying these tools to biotechnology.”





Nature Chemical Biology: A new way to edit the genes of human cells!

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