CRISPR/Cas systems have undergone tremendous advancement in the past decade. These precise genome editing tools have applications ranging from transgenic crop development to gene therapy and beyond. And with their recent development of CRISPR-COPIES, researchers at the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) are further improving CRISPR's versatility and ease of use. Gene editing has revolutionized scientists' capabilities in understanding and manipulating genetic information. This form of genetic engineering allows researchers to introduce new traits into an organism. With CRISPR/Cas systems, researchers can make precise, targeted genetic edits. However, locating optimal integration sites in the genome for these edits has been a critical and largely unsolved problem.

 

Historically, when researchers needed to determine where to target their edits, they would typically manually screen for potential integration sites, then test the site by integrating a reporter gene to assess its cellular fitness and gene expression levels. It's a time- and resource-intensive process. To address this challenge, the CABBI team developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool can identify genome-wide neutral integration sites for most bacterial and fungal genomes within two to three minutes.