Rapid advances with zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) have transformed our ability to make targeted gene knockouts in zebrafish. Tools and techniques for making ZFN- or TALEN-mediated knockouts are becoming well refined and broadly distributed. Efforts supported by this grant over the previous three years have resulted in the development of publicly available protocols, reagents, and software for engineering ZFNs and TALENs and have generated zinc finger arrays and TALENs for a large set of endogenous zebrafish genes. As a result, today almost any zebrafish investigator can knock out their genes of interest using these resources. Despite the importance of gene knockouts for understanding gene function, null alleles represent only one tool for biological research in zebrafish. To understand gene function completely, methods for controlling gene expression both spatially and temporally would provide powerful tools. Engineered zinc finger and transcription activator-like effector repeat DNA-binding domains have the potential to contribute to all of these areas and to thereby further enhance the utility of the zebrafish as an experimental model. In this renewal application, we propose to continue our highly productive collaborative efforts and to move beyond routine gene knockouts to explore additional novel applications for engineered DNA-binding domains in the zebrafish. During the project period, several novel applications for TALEs will be developed, including the creation of artificial transcription factors, the construction of a set of TALENs tha will enable disruption of all zebrafish microRNAs, and the generation of several different types of conditional alleles.
The specific aims are:
Aim 1 : To develop TALE-based transcription factors for controlling endogenous gene expression in zebrafish.
Aim 2 : To generate a comprehensive set of TALENs targeted to all zebrafish microRNAs (miRNAs).
Aim 3 : To develop novel tools that enable conditional alteration of gene structure and expression. By completing these aims, we will advance the field of genome editing and substantially enhance the utility of the zebrafish as an experimental model. Consistent with our strong and well-established commitment to "open-source" science, we will continue to make all of the reagents, protocols, and software needed to practice the technologies developed in this proposal publicly available to academic researchers. We believe that the team of researchers for this proposal has a strong track record of productivity working together and of generating tools and reagents that will be broadly useful to the community.

Public Health Relevance

Transcription activator-like effector (TALE) nucleases have transformed our ability to perform reverse genetics studies in zebrafish, an important model organism for studying human development and disease. The experiments of this proposal will advance and expand the toolbox of TALE-based technologies available for studying zebrafish including the development of artificial transcription factors, the generation of a comprehensive set of nucleases for disrupting the expression of zebrafish micro RNAs, and the optimization of several technologies for creating conditional alleles. Successful completion of the aims of this proposal will substantially enhance the utility of the zebrafish as an experimental model and provide important advances in the field of genome editing.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM088040-05
Application #
8548014
Study Section
Special Emphasis Panel (ZRG1-CB-Z (56))
Program Officer
Sledjeski, Darren D
Project Start
2009-08-01
Project End
2017-07-31
Budget Start
2013-08-01
Budget End
2014-07-31
Support Year
5
Fiscal Year
2013
Total Cost
$561,811
Indirect Cost
$238,931
Name
Massachusetts General Hospital
Department
Type
DUNS #
073130411
City
Boston
State
MA
Country
United States
Zip Code
02199
Tsai, Shengdar Q; Zheng, Zongli; Nguyen, Nhu T et al. (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33:187-97
Hwang, Woong Y; Peterson, Randall T; Yeh, Jing-Ruey Joanna (2014) Methods for targeted mutagenesis in zebrafish using TALENs. Methods 69:76-84
Gonzales, Andrew P W; Yeh, Jing-Ruey Joanna (2014) Cas9-based genome editing in zebrafish. Methods Enzymol 546:377-413
Sander, Jeffry D; Joung, J Keith (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32:347-55
Fu, Yanfang; Sander, Jeffry D; Reyon, Deepak et al. (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32:279-84
Liu, Yang; Kretz, Colin A; Maeder, Morgan L et al. (2014) Targeted mutagenesis of zebrafish antithrombin III triggers disseminated intravascular coagulation and thrombosis, revealing insight into function. Blood 124:142-50
Tsai, Shengdar Q; Wyvekens, Nicolas; Khayter, Cyd et al. (2014) Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 32:569-76
Joung, J Keith; Sander, Jeffry D (2013) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14:49-55
Li, Xianghong; Burnight, Erin R; Cooney, Ashley L et al. (2013) piggyBac transposase tools for genome engineering. Proc Natl Acad Sci U S A 110:E2279-87
Hwang, Woong Y; Fu, Yanfang; Reyon, Deepak et al. (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31:227-9

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