A new approach promises to improve precision genome editing by profiling how individual genes affect DNA sequences.
The ability to make programmed changes to the genomes of living cells has tremendous potential to address a host of unmet medical needs. Over the past decade, enzymes repurposed from bacteria (CRISPR-Cas) have enabled specific gene targeting and genome editing.
Despite recent advances, these techniques remain imprecise, and unwanted mutations frequently occur. Genome editing requires first damaging the DNA — for example, by making a break in the molecular strand — to permit the insertion, deletion or replacement of a gene sequence. Unwanted mutations typically arise from the same processes that make the desired changes, namely, host-cell mechanisms of DNA repair. These mechanisms are highly complex and thus the precision of sequence changes has been hard to control.
To address this challenge, Adamson, together with academic and biotechnology industry collaborators, developed a new experimental and computational approach called Repair-seq, which reveals in exquisite detail how genome-editing tools work.
Repair-seq allows researchers to probe the contribution of individual pathways to repair of specific DNA lesions at sites targeted by genome editors. It works by simultaneously profiling how hundreds of individual genes affect the DNA sequence. Adamson and colleagues have applied their method to three of the most common and promising genome editing approaches. By understanding the biology underlying these tools, the team has pioneered significant improvements.
“We’ve known for a long time that to change the sequence of DNA you first have to break it, but the processes downstream of this damage are incredibly complex and thus often difficult to untangle.” — Britt Adamson
Jeffrey Hussmann, University of California-San Francisco; Peter Chen and David Liu, Broad Institute of MIT and Harvard
Mandana Arbab, Broad Institute of MIT and Harvard; Luke Koblan and Jonathan Weissman, Whitehead Institute for Biomedical Research, MIT; Max Shen, Genentech; Cecilia Cotta-Ramusino, Tessera Therapeutics
Postdoctoral Research Associate Jia Ling, Research Specialist II Purnima Ravisankar, and Graduate Student Jun Yan.
Patent pending. Princeton is seeking outside interest in developing this technology.
National Institutes of Health, National Science Foundation
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