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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM063904-11
Application #
8658832
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Hoodbhoy, Tanya
Project Start
2001-09-01
Project End
2016-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
11
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Mayo Clinic, Rochester
Department
Type
DUNS #
City
Rochester
State
MN
Country
United States
Zip Code
55905
Ma, Alvin C; McNulty, Melissa S; Poshusta, Tanya L et al. (2016) FusX: A Rapid One-Step Transcription Activator-Like Effector Assembly System for Genome Science. Hum Gene Ther 27:451-63
Zeituni, Erin M; Wilson, Meredith H; Zheng, Xiaobin et al. (2016) Endoplasmic Reticulum Lipid Flux Influences Enterocyte Nuclear Morphology and Lipid-dependent Transcriptional Responses. J Biol Chem 291:23804-23816
Hatzold, Julia; Beleggia, Filippo; Herzig, Hannah et al. (2016) Tumor suppression in basal keratinocytes via dual non-cell-autonomous functions of a Na,K-ATPase beta subunit. Elife 5:
Jeradi, Shirine; Hammerschmidt, Matthias (2016) Retinoic acid-induced premature osteoblast-to-preosteocyte transitioning has multiple effects on calvarial development. Development 143:1205-16
Richardson, Rebecca; Metzger, Manuel; Knyphausen, Philipp et al. (2016) Re-epithelialization of cutaneous wounds in adult zebrafish combines mechanisms of wound closure in embryonic and adult mammals. Development 143:2077-88
Ding, Yonghe; Long, Pamela A; Bos, J Martijn et al. (2016) A modifier screen identifies DNAJB6 as a cardiomyopathy susceptibility gene. JCI Insight 1:
Zhao, Yu; Wang, Liguo; Ren, Shancheng et al. (2016) Activation of P-TEFb by Androgen Receptor-Regulated Enhancer RNAs in Castration-Resistant Prostate Cancer. Cell Rep 15:599-610
Leibold, Sandra; Hammerschmidt, Matthias (2015) Long-term hyperphagia and caloric restriction caused by low- or high-density husbandry have differential effects on zebrafish postembryonic development, somatic growth, fat accumulation and reproduction. PLoS One 10:e0120776
Bedell, Victoria M; Ekker, Stephen C (2015) Using engineered endonucleases to create knockout and knockin zebrafish models. Methods Mol Biol 1239:291-305
Craig, Michael P; Grajevskaja, Viktorija; Liao, Hsin-Kai et al. (2015) Etv2 and fli1b function together as key regulators of vasculogenesis and angiogenesis. Arterioscler Thromb Vasc Biol 35:865-76

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