New forms of CRISPR with applications in biotechnology

2017

Challenge

CRISPR-based technologies derived from the immune systems of bacteria have revolutionized genome engineering by permitting the selective insertion and deletion of genetic information in a strand of DNA. However, the available CRISPR-based methods still have many drawbacks and limitations, including the potential for unwanted changes in other parts of the genome and difficulties with editing RNA rather than DNA. As a result, there is high demand for alternative CRISPR-based systems.

Advance

IRP researchers led by Eugene V. Koonin, Ph.D., developed computational approaches to identify new CRISPR systems by mining microbial genomes. As a result, several novel variants of CRISPR have been discovered, some of which specifically target RNA. One of these variants was used to create a tool, called Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK), that can be used to detect specific DNA or RNA sequences, such as those associated with Zika virus, certain dangerous bacteria, and cancers.

Impact

The discovery of these new CRISPR-based systems has led to the development of two powerful methods for RNA detection and modification. Additionally, comparing new and previously known CRISPR variants sheds light on the fundamental biology and evolution of microbial adaptive immunity.

Publications

Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV. Diversity and evolution of class 2 CRISPR-Cas systems. (2017). Nat Rev Microbiol. 15(3):169-182.

Smargon AA, Cox DBT, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, Abudayyeh OA, Essletzbichler P, Shmakov S, Makarova KS, Koonin EV, Zhang F. Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28. (2017). Mol Cell. 65(4):618-630.

Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F. Nucleic acid detection with CRISPR-Cas13a/C2c2. (2017). Science. 356(6336):438-442.