International Zebrafish Mutagenic Protein Trap

Project: Research project

Description

DESCRIPTION (provided by applicant): The zebrafish (Danio rerio) is the preeminent non-mammalian vertebrate system for the study of core vertebrate biology and behavior and for the modeling of human disease. Collections of molecularly characterized mutant lines have been powerful enabling tools for the nematode, fly and mouse fields. Genomic approaches have robustly characterized the nuclear genome and transcriptome. However, the genomic assessment of the full complexity of the proteome in a dynamic context and in vivo is still largely unknown. The zebrafish offers the first comprehensive analysis of the proteome using as template an entire vertebrate genome. We show that mutagenic protein trap gene-breaking transposons (GBTs) are effective and conditional loss- of-function tools for exploring traditional areas such as the biology of development (including organogenesis) but also open up new options including the genetics of behavior such as the biology of the nicotine response. This application is in response to "PAR-08-139 Enhancing Zebrafish Research with Research Tools and Techniques (R01)" to establish a large-scale collection of these conditional mutant alleles for the zebrafish community through a coordinated international effort. We will deliver the following at project's end: I. 2000 new mutagenic protein trap GBT zebrafish lines with basic description of the tagged expression patterns will be established and made available in real-time through the searchable online database zfishbook.org. These lines are immediately available through distribution by the Mayo Clinic Zebrafish Core Facility. II. We will conduct molecular analyses of these lines and subsequent annotation on the zebrafish genome project to identify the trapped proteins in this collection. We will initially expand the use of established 5'RACE protocols to identify trapped protein-encoding mRNA. We will subsequently engage next generation sequence techniques followed by linkage analysis to potentially accelerate the process of mapping GBT insertions. All sequence information will be initially distributed through zfishbook.org and then integrated in ZFIN, Fishmap and other zebrafish genomic databases. III. We will regularly synchronize this collection with the Zebrafish International Resource Center (ZIRC) for long-term archival and distribution to the zebrafish community. We will use a recently established 2D barcoding inventory system with a state-of-the-art sperm cryopreservation approach to facilitate regular shipping of new lines to ZIRC. This proposal is to establish a molecularly characterized collection, in silico catalog and distribution network of conditional mutations for the preeminent non-mammalian vertebrate, the zebrafish. These dominantly marked mutant lines also represent an ideal substrate for large-scale behavioral and other phenotypic assessment of the genome as a part of the recently launched phenome project for the zebrafish. PUBLIC HEALTH RELEVANCE: This proposal is to generate a mutant resource of 2000 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. These fish lines are available in real-time through distribution by the Mayo Clinic Zebrafish Core Facility. The full collection will be established through a coordinated international effort and archived and distributed by the Zebrafish International Resource Center for use by all zebrafish researchers worldwide.
StatusFinished
Effective start/end date8/1/114/30/17

Funding

  • National Institutes of Health: $500,001.00
  • National Institutes of Health: $48,560.00
  • National Institutes of Health: $569,740.00
  • National Institutes of Health: $509,396.00
  • National Institutes of Health: $487,501.00
  • National Institutes of Health: $553,242.00
  • National Institutes of Health: $562,333.00
  • National Institutes of Health: $48,560.00

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Zebrafish Proteins
Zebrafish
Vertebrates
Genome
Proteome
Databases
Proteins
Alleles

ASJC

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)