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News / 10.22.15

International team characterizes three potential alternatives to Cas9

By NIH Communications

An international team of CRISPR-Cas researchers has identified three new naturally-occurring systems that show potential for genome editing. The discovery and characterization of these systems is expected to further expand the genome editing toolbox, opening new avenues for biomedical research. The research, published today in the journal Molecular Cell, was supported in part by the National Institutes of Health.

“This work shows a path to discovery of novel CRISPR-Cas systems with diverse properties, which are demonstrated here in direct experiments,” said Eugene Koonin, Ph.D., senior investigator at the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), part of the NIH. “The most remarkable aspect of the story is how evolution has achieved a broad repertoire of biological activities, a feat we can take advantage of for new genome manipulation tools.”

Enzymes from the CRISPR system are revolutionizing the field of genomics, allowing researchers to target specific regions of the genome and edit DNA at precise locations. “CRISPR” stands for Clustered Regularly Interspaced Short Palindromic Repeats, which are key components of a system used by bacteria to defend against invading viruses. Cas9 – one of the enzymes produced by the CRISPR system – binds to the DNA in a highly sequence-specific manner and cuts it, allowing precise manipulation of a region of DNA. Enzymes such as Cas9 provide researchers with a gene editing tool that is faster, less expensive and more precise than previously developed methods.

The three newly-characterized systems share some features with Cas9 and Cpf1, a recently characterized CRISPR enzyme, but have unique properties that could potentially be exploited for novel genome editing applications. This study highlights the diversity of CRISPR systems, which can be leveraged to develop more efficient, effective, and precise ways to edit DNA.

The researchers took a novel bioinformatics approach to discover the new proteins, provisionally termed C2c1, C2c2, and C2c3, developing a series of computational approaches to search NIH genomic databases and identify new CRISPR-Cas systems. In addition to Koonin, the research team included Feng Zhang of the Broad Institute of MIT and Harvard and the McGovern Institute for Brain Research at MIT, Konstantin Severinov of Rutgers University - New Brunswick, and the Skolkovo Institute of Science and Technology, graduate student Omar Abudayyeh of the Harvard-MIT Division of Health Sciences and Technology, and NCBI’s Kira Makarova, Sergey Shmakov (also at Skolkovo Institute of Science and Technology), and Yuri Wolf.

“There are multiple ways to modify the search algorithm, so more exciting and distinct CRISPR-Cas mechanisms should be expected soon,” said Severinov. “These new mechanisms will undoubtedly attract the attention of basic and applied scientists alike.”

Initial experimental work exploring the function of these proteins reveals that they are substantially different from the well-characterized Cas9 protein, which has been widely used for genome editing.

With the analysis of C2c1, C2c2, and C2c3, the team was able to infer the intricate evolutionary pathway of these adaptive defense systems.

“The collaborative nature of this work highlights the power of bringing together top scientists with diverse strengths to innovate at the interface of computation, molecular biology and evolutionary biology,” said Zhang.

The Koonin and Zhang groups also recently collaborated on a project that resulted in the characterization of Cpf1, a novel CRISPR nuclease that is expected to become an important genome editing tool.

• Feng Zhang, of the Broad Institute and MIT, is supported by the National Institute of Mental Health (5DP-MH100706 and 1R01-MH110049) and by the National Institute of Diabetes and Digestive and Kidney Diseases (5R01DK097760-03).
• Konstantin Severinov, of Rutgers University and the Skolkovo Institute of Science and Technology, is supported by National Institute of General Medical Sciences (GM10407).

Paper cited: Shmakov, S., Abudayyeh, O. et al. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Molecular Cell. DOI: http://dx.doi.org/10.1016/j.molcel.2015.10.008

About the National Center for Biotechnology Information (NCBI)
NCBI creates public databases in molecular biology, conducts research in computational biology, develops software tools for analyzing molecular and genomic data, and disseminates biomedical information, all for the better understanding of processes affecting human health and disease. NCBI is a division of the National Library of Medicine. For more information, visit http://www.ncbi.nlm.nih.gov.

About the National Library of Medicine (NLM)
The world’s largest biomedical library, NLM maintains and makes available a vast print collection and produces electronic information resources on a wide range of topics that are searched billions of times each year by millions of people around the globe. It also supports and conducts research, development, and training in biomedical informatics and health information technology. Additional information is available at http://www.nlm.nih.gov.

About the National Institutes of Health (NIH)
NIH, the nation's medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.

About the Broad Institute of MIT and Harvard
The Eli and Edythe L. Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community.

Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to broadinstitute.org.