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Easier, Safer Genome Editing

Ashley Yeager

How can a microbe’s immune system make editing the genomes of mammalian cells easier and safer? Find out...

Enzymes and RNA from prokaryotic immune systems may make genome editing of mammalian cells—including humans cells—easier and safer, according to two new studies.

In papers published on January 3 in Science (1–2), two teams reported the development of genome editing tools from clustered regularly interspaced short palindromic repeats (CRISPR), which are sequences in bacteria and archaea that provide a form of acquired immunity to foreign DNA by enabling recognition and cleavage of foreign nucleic acids. The teams from MIT and Harvard University used the microbial CRISPR enzymes and RNA from Streptococcus pyogenes and Streptococcus thermophiles to insert, cleave, repair, and edit DNA in mouse and human cells.

Genome engineering with CRISPR/Cas nucleases shows that different Cas9 enzymes, depicted with different colored scissors, target distinct locations in the genome. Source: Feng Zhang, MIT.

"It is amazing how well the [CRISPR] system works, even though the enzymes and RNA have been taken from bacterial cells and introduced into mammalian cells," says MIT chemist and bioengineer Feng Zhang, who led one of the studies.

In their paper, Zhang and colleagues used bacterial RNA to guide bacterial Cas9 nucleases to specific loci in the mouse and human genomes, leading to precisely targeted strand breaks. In the other paper, Harvard geneticist George Church and his collaborators used the CRISPR method to edit the genomes of several different human cell lines, including induced pluripotent stem cells.

The Cas9 nuclease was identified last year by a team of researchers from the Lawrence Berkeley National Laboratory who realized the enzyme’s potential genome-editing applications. The two new papers, however, are the first demonstrations of Cas9 nucleases used to edit the genomes of mammalian cells.

Based on the new results, Zhang believes that CRISPR could have significant advantages over other genome-engineering technologies such as zinc finger nucleases (ZFNs) or transcription activator-like effector nucleases (TALENS). "CRISPR is much easier to use and more scalable," Zhang said.

In addition, CRISPR can simultaneously target multiple sites in the same cell, which is difficult to do with ZFNs or TALENs. This feature may be helpful in the study of multiple disease-associated mutations, which likely function together rather than alone to cause disease. "In order to identify the causal group of mutations, we have to be able to simultaneously introduce multiple mutations into the genome," Zhang said.

And finally, the CRISPR system may be a safer and less toxic genome-engineering alternative. Zhang’s team engineered a mutant version of Cas9 that nicks the DNA instead of making a double-strand break. Because the mutagenic process that repairs breaks is less likely to fix nicks, this may make CRISPR genome editing suitable for therapeutic applications.


1. Cong, L. et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science Express. 03 Jan. pp 1-7.

2. Mali, P. et al. 2013. RNA-guided human genome engineering via Cas9. Science Express. 03 Jan. pp. 1-5.

Keywords:  genome editing