Unbiased forward genetic screens play a central role in model organism genetics. C. elegans screens have contributed to some of the most important discoveries in biology in the last 35 years: Ras - MAP kinase pathways, cell death pathways, RNA interference and posttranscriptional regulation by microRNAs are examples. However, only ~10% of genes have alleles that have been isolated in forward screens. We propose to develop a transposon-based gene trap that will simultaneously generate balanced knockout alleles and cellular expression patterns. As a complement to this method, we will design constructs and methods to standardize and lower the costs of CRISPR-based gene traps. Although C. elegans has possibly the most thoroughly characterized anatomy of any organism, worm genetics has been confounded by the difficulty of unambiguously assigning expression of a specific gene to a particular cell. We will generate worm strains and open-source microscope hardware that will aid individual users as well as automated systems in solving this final step in assigning gene expression patterns. As a package, the methods will propose to develop will be a resource for the whole C. elegans research community.
Aim 1. Random gene traps. We will modify the Mos1 transposon from Drosophila so that it will act as a gene trap when inserted into the C. elegans genome, that is, disrupt the gene and report the gene expression pattern with tagRFP.
Aim 2. Directed gene traps. We will design and test a high-throughput strategy for targeted gene traps using CRISPR. The library of clones generated in this aim can be also be used by individual labs to obtain the expression pattern and a null allele of any gene in the genome.
Aim 3. Expression pattern toolkit. We will build nematode strains and microscopy hardware for high-throughput recording and analyzing the expression patterns of genes in 3D. These tools will be applied to the gene traps but will also be of use to the C. elegans community for cell expression identities, particularly in the brain of the worm.

Public Health Relevance

The nematode C. elegans is one of the major model organisms for studies of cell biology; currently there are 747 funded NIH grants that use C. elegans. These labs pursue projects studying genes involved in aging, cancer, toxicology, neuroscience, and response to pathogens. The ability to rapidly screen for genes expressed in specific cell types and to efficiently generate a collection of gene knock-outs will add a significant tool to the researchers toolkits. This will make experimentation much faster and results more reliable for studies of all aspects of human health.

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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Willis, Kristine Amalee
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University of Utah
Schools of Arts and Sciences
Salt Lake City
United States
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Frøkjær-Jensen, Christian; Jain, Nimit; Hansen, Loren et al. (2016) An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline. Cell 166:343-357
Schwartz, Matthew L; Jorgensen, Erik M (2016) SapTrap, a Toolkit for High-Throughput CRISPR/Cas9 Gene Modification in Caenorhabditis elegans. Genetics 202:1277-88
Wheeler, Bayly S; Anderson, Erika; Frøkjær-Jensen, Christian et al. (2016) Chromosome-wide mechanisms to decouple gene expression from gene dose during sex-chromosome evolution. Elife 5:
Edelman, Theresa L B; McCulloch, Katherine A; Barr, Angela et al. (2016) Analysis of a lin-42/period Null Allele Implicates All Three Isoforms in Regulation of Caenorhabditis elegans Molting and Developmental Timing. G3 (Bethesda) 6:4077-4086
Frøkjær-Jensen, Christian (2015) Transposon-Assisted Genetic Engineering with Mos1-Mediated Single-Copy Insertion (MosSCI). Methods Mol Biol 1327:49-58
Frøkjær-Jensen, Christian; Davis, M Wayne; Sarov, Mihail et al. (2014) Random and targeted transgene insertion in Caenorhabditis elegans using a modified Mos1 transposon. Nat Methods 11:529-34
Frøkjær-Jensen, Christian (2013) Exciting prospects for precise engineering of Caenorhabditis elegans genomes with CRISPR/Cas9. Genetics 195:635-42
Frøkjær-Jensen, Christian; Davis, M Wayne; Ailion, Michael et al. (2012) Improved Mos1-mediated transgenesis in C. elegans. Nat Methods 9:117-8
Zeiser, Eva; Frøkjær-Jensen, Christian; Jorgensen, Erik et al. (2011) MosSCI and gateway compatible plasmid toolkit for constitutive and inducible expression of transgenes in the C. elegans germline. PLoS One 6:e20082