The past five years have seen extraordinary advances in genome engineering technologies, yet we still lack efficient, robust tools for precise genome manipulation, particularly the ability to insert a desired sequence at a target site. Such tools would revolutionize our approach to treating human diseases and significantly increase the pace of functional genetic studies throughout the biological sciences. Current approaches are focused on the development of nucleases, such as TALENs, zinc-fingers, and Cas proteins, but there is a limit to the utility of these enzymes and they all rely on the host endogenous DNA repair machinery. Moreover, the use of a nuclease to achieve therapeutic gene editing requires additional efforts to safeguard against off-target mutagenic events. A partial solution to this challenge already exists in the form of mobile genetic elements (MGEs), systems that microbes have been using (or fighting) for millennia to achieve precise genome manipulation. We will explore the diverse pool of MGEs and identify those with characteristics that can be leveraged for eukaryotic genome editing. Precision genome manipulation can be broadly divided into three subcategories: insertions, deletions, and rearrangements, each of which forms the foundation for an array of applications. Our approach will be to consider each of these modes of operation separately to first select candidate MGEs or components of these systems through bioinformatics analysis and extrapolating from known systems. For example, transposases and recombinases may be harnessed for insertions, whereas the RNA-templated genome unscrambling that occurs in the ciliates may be suitable for adaptation for genome rearrangements. Once candidates for these three modes have been identified, we will functionally characterize them in vitro and then develop them for genome editing. Finally, we will assess the specificity, efficacy, and safety of these novel precision genome editors in vivo. This approach represents an innovative new direction in the development of genome engineering technology that overcomes the reliance on nucleases by designing new, self-contained enzymatic tools that can accomplish all three operational modes of genome manipulation. This work will complement our on-going research efforts to develop effective delivery methods for genome engineering components. Together, these technologies will allow us to realize the full potential of genome engineering, particularly as an avenue for treatment of human diseases.

Public Health Relevance

There are more than 5000 human diseases caused by known changes in the genome (i.e., small point mutations, expansions, deletions, and rearrangements), most of which are currently untreatable. In this proposal, we aim to develop a suite of tools designed to achieve precise genome surgery for repairing disease-causing changes based on microbial genetic elements, which have evolved to perform a range of DNA manipulations. The technologies we will develop through this work have the potential to significantly accelerate biomedical research and revolutionize our ability to treat and cure human diseases.

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
NIH Director’s Pioneer Award (NDPA) (DP1)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Yang, Yu-Chung
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Broad Institute, Inc.
United States
Zip Code
Myhrvold, Cameron; Freije, Catherine A; Gootenberg, Jonathan S et al. (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444-448
Gootenberg, Jonathan S; Abudayyeh, Omar O; Kellner, Max J et al. (2018) Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360:439-444
Tekin, Halil; Simmons, Sean; Cummings, Beryl et al. (2018) Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons. Nat Biomed Eng 2:540-554
Cox, David B T; Gootenberg, Jonathan S; Abudayyeh, Omar O et al. (2017) RNA editing with CRISPR-Cas13. Science 358:1019-1027