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Researchers Led by George Church Simplify Powerful CRISP/Cas9 Gene Editing Tool by Developing Interactive Software to Find Guide RNAs Predicted to be Highly Specific and Highly Active for Their Gene Targets

Researchers at Harvard University and the University of California, San Diego (UC San Diego), have developed a new user-friendly resource to accompany the powerful gene editing tool called CRISPR/Cas9, which has been widely adopted to make precise, targeted changes in DNA. This new breakthrough has the potential to facilitate new discoveries in gene therapies and basic genetics research. The research was published online on July 13, 2015 in Nature Methods. The article is titled “Unraveling CRISPR-Cas9 Genome Engineering Parameters via a Library-on-Library Approach.” The study describes a way to simplify a laborious part of the gene-editing process using the CRISPR/Cas9 system: choosing the best components to match specific gene targets. "We've taken a step towards making the CRISPR/Cas9 system more robust," said Dr. Prashant Mali, an Assistant Professor in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering, and a co-first author of the Nature Methods publication. CRISPR/Cas9 is a relatively new genome engineering tool that can target a particular segment of DNA in living cells -- such as a gene mutation -- and replace it with a new genetic sequence. This technology ultimately has applications in gene therapies for genetic disorders such as sickle cell anemia and cystic fibrosis. The CRISPR/Cas9 system has two components: a short "guide RNA" with a sequence matching a particular gene target, and a large protein called Cas9 that cuts DNA precisely at that target. Herein lies the beauty of the CRISPR/Cas9 system: to target another region of the genome, researchers can simply change the guide RNA sequence to match the new gene target. However, finding the best guide RNA match for a specific gene target is a labor-intensive process. This is because multiple guide RNA sequences can serve as potential matches for each gene target. As a result, researchers might need to test numerous candidates of guide RNAs before finding the most active guide RNA.

To decipher what makes certain guide RNAs better than others, the researchers conducted what they called a "library-on-library" approach, in which they evaluated a library containing thousands of guide RNAs against a library containing thousands of corresponding gene targets. The team analyzed the data from the library-on-library approach to determine patterns among the guide RNAs that were the most active. Using the data and patterns from these thousands of gene targeting experiments, the team developed a new matchmaking software that predicts and ranks the best guide RNA matches for any given gene target.

"From these experiments, we were able to find features in the guide RNAs that worked and in those that didn't work. We built a computational model that accounts for all these different features. The end product is an interactive software for users to find guide RNAs that are predicted to be highly specific and highly active for their gene targets," said Dr. Raj Chari, a research fellow working in the laboratory of Professor George Church in the Department of Genetics at Harvard Medical School, and a co-first author of the study.

Dr. Church (photo), a renowned technical wizard in the area of DNA, was the supervisor of the project and is the senior author of the Nature Methods article.

"We hope to minimize the time and work in finding the most successful guide RNA sequence for a gene target, which will be helpful for finding new gene therapies," said Dr. Chari.

"Overall, this new method offers a simple approach to assess a large number of guide RNAs in a short amount of time. We believe this will be a useful resource for the community towards designing improved genome engineering experiments," added Dr. Mali.

In addition to those mentioned, the article authors include Dr. Mark Moosburner of the Scripps Institute of Oceanography at UC San Diego.

As background on the incredible scientific career of Dr. Church, BioQuick would suggest reading the recent blog posted by eminent nucleic acid scientist Dr. Jerry Zon. That blog is entitled "The Most Interesting Scientist in the World: George M. Church," and it may be found at the following link: http://zon.trilinkbiotech.com/2015/05/12/george-church/.

Dr. Zon, a world-class expert in nucleic acid chemistry, is currently the Director of Business Development at TriLink Biotechnologies (http://www.trilinkbiotech.com/)in San Diego, California. Dr. Zon posts a a highly entertaining and deeply informative biweekly blog for TriLink and this blog is entitled "Zone in with Zon."

[Press release] [Nature Methods abstract]
["The Most Interesting Scientist in the World: George M. Church"--Zone in with Zon blog post, May 12, 2015]