New method giving insight into DNA repair pathways could improve genome editing

25 October 2021

In-depth mapping of DNA repair mechanisms of the double-stranded and single-stranded breaks required for genome editing, could enhance the efficacy of these approaches, new research has revealed.

Scientists at Princeton University, New Jersey, and Massachusetts Institute of Technology (MIT) have published research untangling the complex mechanisms controlling DNA repair in cells using a new sequencing method. Genome editing using CRISPR relies on cells’ own mechanisms to repair DNA breaks after edits are made. A better understanding of these processes might help reduce off-target mutations and increase the accuracy of the approach.

Dr Jeffrey Hussmann, first author of the study published in the journal Cell, said: ‘The field of [genome] editing has moved so quickly, and people have been so creative developing new methods that our ability to apply them has dramatically outpaced our understanding of exactly how they work.’

The team used a form of CRISPR they had already developed called CRISPRi (CRISPR interference) to turn off hundreds of genes known to be involved in DNA repair while simultaneously inducing a set of predetermined mutations across the genome. The paper then explains how authors used a new method they called Repair-seq to sequence the mutations that occurred when various repair genes were switched off. This allowed them to find out which different genes work together to repair specific DNA breaks and how different genome editing approaches might affect this.

They used the findings to map the mutations caused by prime editing, a genome editing approach developed by one of the labs involved in the research (see BioNews 1021). When authors inhibited a repair pathway they found to be behind these mutations the performance of prime editing was shown to improve. The team published the findings from this in another paper, also in Cell.

‘This combination of different CRISPR-based technologies has made it possible to, in one fell swoop, recapitulate a lot of the work that was done painstakingly over the past decades to study each repair pathway one at a time,’ Dr Hussmann said. 

He continued: ‘The high-level view of repair that our method produces shows us many of the things that people saw before, and at the same time reveals unexpected connections that we only get by having the comprehensive picture.’

The team hopes that their data will lead to an increase in the accuracy of genome editing as well as a greater understanding of how cells repair damaged DNA. Enabling more accurate genome editing could make its use safer and more effective in medical applications.

Dr Britt Adamson of Princeton University and lead author of the study remarked: ‘It has been rewarding to see the efforts of our collaboration come together… We hope the insights from our study and tools that those insights have led to will be widely useful to the research community.’