The zebrafish has emerged as a premier model organism for the study of human development and disease. Its greatest asset is that it is a genetic system in which mutant phenotypes can be effectively dissected at the organismal, cellular and subcellular levels. Many forward genetic screens have identified genes and subsequently delineated their roles in embryonic cell fate specification, patterning, morphogenesis and organogenesis. However with the sequencing of the zebrafish genome we now know that many genes have never been identified by forward genetics, so their role in development remains an open question. Furthermore, recent explosion in the identification of human disease-causing genes has the potential to re-purpose the zebrafish as a leading model for human genetic disease, provided the zebrafish homologs of these genes can be mutated within the next few years. A number of reverse genetics approaches are currently being pursued in the zebrafish, with the potential to generate knock-outs in many of the genes in the genome. However, these approaches are largely untargeted and therefore do not address the immediate and pressing needs of the scientific community. We have created a large library of 15,456 cryopreserved, ENU mutagenized fish and estimate that this library contains at least one nonsense allele in any average-sized zebrafish gene with 97% chance. We have developed methodologies to screen this library efficiently for mutations that are present in a single heterozygous fish, and using these methodologies we have identified one or more nonsense mutations in over 80 genes considered to be of high-priority by zebrafish researchers. We have distributed these mutants widely within the community, resulting in 18 publications in the past four years. We have now transitioned to innovative and high-throughput Illumina sequencing methodologies for mutation detection with which we propose to identify one or more loss-of-function mutation in over 300 zebrafish genes in three years, and to deliver them to the community via ZIRC.

Public Health Relevance

The goal of this grant is to mutate zebrafish genes whose human homologs play important roles in development and disease, and to provide those mutants to the community. Using these mutants and the other attributes of this animal model (its fecundity, external development and optical qualities) researchers will be able to discover mechanisms underlying normal development and disease pathogenesis.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Research Project (R01)
Project #
5R01HD076585-08
Application #
8548388
Study Section
Special Emphasis Panel (ZRG1-CB-Z (56))
Program Officer
Javois, Lorette Claire
Project Start
2003-08-22
Project End
2015-08-31
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
8
Fiscal Year
2013
Total Cost
$610,976
Indirect Cost
$140,408
Name
Fred Hutchinson Cancer Research Center
Department
Type
DUNS #
078200995
City
Seattle
State
WA
Country
United States
Zip Code
98109
Stawicki, Tamara M; Hernandez, Liana; Esterberg, Robert et al. (2016) Cilia-Associated Genes Play Differing Roles in Aminoglycoside-Induced Hair Cell Death in Zebrafish. G3 (Bethesda) 6:2225-35
Shah, Arish N; Moens, Cecilia B (2016) Approaching Perfection: New Developments in Zebrafish Genome Engineering. Dev Cell 36:595-6
Rossi, Andrea; Gauvrit, Sebastien; Marass, Michele et al. (2016) Regulation of Vegf signaling by natural and synthetic ligands. Blood :
Nishioka, Tatsuji; Arima, Naoaki; Kano, Kuniyuki et al. (2016) ATX-LPA1 axis contributes to proliferation of chondrocytes by regulating fibronectin assembly leading to proper cartilage formation. Sci Rep 6:23433
Shah, A N; Moens, C B; Miller, A C (2016) Targeted candidate gene screens using CRISPR/Cas9 technology. Methods Cell Biol 135:89-106
Dubrulle, Julien; Jordan, Benjamin M; Akhmetova, Laila et al. (2015) Response to Nodal morphogen gradient is determined by the kinetics of target gene induction. Elife 4:
Li-Villarreal, Nanbing; Forbes, Meredyth M; Loza, Andrew J et al. (2015) Dachsous1b cadherin regulates actin and microtubule cytoskeleton during early zebrafish embryogenesis. Development 142:2704-18
Miller, Adam C; Voelker, Lisa H; Shah, Arish N et al. (2015) Neurobeachin is required postsynaptically for electrical and chemical synapse formation. Curr Biol 25:16-28
Pan, Luyuan; Shah, Arish N; Phelps, Ian G et al. (2015) Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis. BMC Genomics 16:83
Shah, Arish N; Davey, Crystal F; Whitebirch, Alex C et al. (2015) Rapid reverse genetic screening using CRISPR in zebrafish. Nat Methods 12:535-40

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