The vertebrate genome contains a predicted 20,000+ genes, many of unknown biological role(s). In addition, a large fraction of these molecules have distinct functions in diverse processes. The functional annotation of genes is one of the major next steps in understanding the vertebrate genome. Indeed, despite over a decade after the completion of the human genome effort, the diversity of genes undergoing active research has not substantially changed. We have developed a collection of gene-break transposon (GBT) alleles for use in phenotypic annotation of the vertebrate genome using the preeminent non-mammalian model organism, the zebrafish (Danio rerio). GBTs represent an innovative methodology to ask current questions while also serving as a platform for new scientific query. We will use our ongoing 500 GBT collection as a platform of candidate gene mutations for assessment of the vertebrate phenome. In this competitive renewal, we will focus on the annotation of biological function to identify new players in development as well as a set of clinically relevant biological processes. We will accomplish this goal through the following specific aims:
Specific Aim I. We will conduct phenotypic annotation of 500+ GBT lines for genes required for zebrafish embryonic and early larval development.
Specific Aim II. We will conduct phenotypic annotation of skin-expressed proteins required for formation of the integument during development and for genes required for the skin's wound healing response.
Specific Aim III : We will identify cardiac mutants for annotation of gene functions in either cardiogenesis or adult cardiomyopathy.
Specific Aim I V. We will identify genes required for digestive organ formation, lipid metabolism and lipid signaling.
Specific Aim V. Recording of GBT gene function annotation using PATO-compliant phenotypic assessment description and integration into ongoing zebrafish functional databases including zfishbook and ZFIN. We selected embryonic development due to the advantages of external development of the zebrafish, cardiac biology and function due to the critical role of heart disease as the leading cause of death in the US, integument biology due to the strong impact of skin disease on one in three Americans, and lipid biology in development and physiology due to its critical role(s) in development, heart disease and obesity. Together, this project will annotate a panel of new genes for the better understanding of human health and disease.

Public Health Relevance

This proposal is to phenotypically annotate 500+ vertebrate genes using an ongoing mutant resource of new conditional protein trap mutations for the zebrafish (Danio rerio), the preeminent non-mammalian system for the study of core vertebrate biology and for modeling of human disease. This program will identify new genes involved in development, skin biology including regeneration, heart development and disease, and GI organ formation and lipid biochemistry.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Hoodbhoy, Tanya
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Mayo Clinic, Rochester
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Miyares, Rosa L; de Rezende, Vitor B; Farber, Steven A (2014) Zebrafish yolk lipid processing: a tractable tool for the study of vertebrate lipid transport and metabolism. Dis Model Mech 7:915-27
Wu, X; Blackburn, P R; Tschumper, R C et al. (2014) TALEN-mediated genetic tailoring as a tool to analyze the function of acquired mutations in multiple myeloma cells. Blood Cancer J 4:e210
Fischer, Boris; Metzger, Manuel; Richardson, Rebecca et al. (2014) p53 and TAp63 promote keratinocyte proliferation and differentiation in breeding tubercles of the zebrafish. PLoS Genet 10:e1004048
He, Bai-Liang; Shi, Xiangguo; Man, Cheuk Him et al. (2014) Functions of flt3 in zebrafish hematopoiesis and its relevance to human acute myeloid leukemia. Blood 123:2518-29
Richardson, Rebecca; Slanchev, Krasimir; Kraus, Christopher et al. (2013) Adult zebrafish as a model system for cutaneous wound-healing research. J Invest Dermatol 133:1655-65
Miyares, Rosa Linda; Stein, Cornelia; Renisch, Bjorn et al. (2013) Long-chain Acyl-CoA synthetase 4A regulates Smad activity and dorsoventral patterning in the zebrafish embryo. Dev Cell 27:635-47
Otis, Jessica P; Farber, Steven A (2013) Imaging vertebrate digestive function and lipid metabolism in vivo. Drug Discov Today Dis Models 10:
Bedell, Victoria M; Person, Anthony D; Larson, Jon D et al. (2012) The lineage-specific gene ponzr1 is essential for zebrafish pronephric and pharyngeal arch development. Development 139:793-804
Clark, Karl J; Argue, David P; Petzold, Andrew M et al. (2012) zfishbook: connecting you to a world of zebrafish revertible mutants. Nucleic Acids Res 40:D907-11
Bedell, Victoria M; Westcot, Stephanie E; Ekker, Stephen C (2011) Lessons from morpholino-based screening in zebrafish. Brief Funct Genomics 10:181-8

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