# Genome engineering in the nematode C. elegans

> **NIH NIH R01** · UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH · 2024 · $317,240

## Abstract

Project Summary
 CRISPR offers the promise of total control over genes in model organisms, such as the nematode
C. elegans. To make this a reality, we need functional tags on all proteins that we can use as handles to
influence the biology of any cell. However, each individual edit requires unique reagents and takes experienced
worm geneticists 6 weeks or more to create. To edit many genes with diverse tags one gene at a time is just
not practical. The goals of this project are to make CRISPR genome modifications simple, inexpensive and
with increased throughput. We propose a series of multiplexed genome engineering methods that will
accelerate gene tagging in C. elegans 10- to 100-fold. First, we propose to optimize cassette exchange
methods using diverse recombinases that will allow geneticists to alter one gene with many diverse tags.
Second, we propose to develop a multiplexed CRISPR strategy that will allow groups to modify many genes
within a single editing experiment. Third, we will develop software and reagent libraries required to modify all
genes in the genome.
 • Aim 1. One gene: recombinase-mediated cassette exchange. We will characterize the germline activity
of a diverse set of recombinases and develop cassette exchange methods for rapidly integrating transgenes
or tags anywhere in the genome.
 • Aim 2. Many genes: multiplex CRISPR. Current methods require a unique injection cocktail for each
unique gene modification. We will develop a multiplex CRISPR strategy in which the reagents for tagging many
unique genes are injected simultaneously to generate many edited worm strains, each with a single edited
target.
 • Aim 3. All genes: software and molecular reagents. To tag the proteome, reagents cannot be efficiently
designed one-at-a-time, by hand. We will write software that identifies optimal tagging locations and designs
the required reagents, and we will build build a cost-effective pooled molecular workflow to build genome editing
reagents.
 C. elegans shares most of the genes mutated in human genetic diseases; as a simple, compact and rapidly
developing animal, it is an attractive platform to study these genes. In the future, the genome engineering
pipelines developed here could be used to insert a swappable tagging site in every protein-coding gene in the
C. elegans genome, making it possible to easily add any tag to any gene. Such a strain collection would be a
boon for cell biologists and geneticists, enabling new inroads in studying how cells work and how to fix them
when disease processes cause them to malfunction.

## Key facts

- **NIH application ID:** 10766800
- **Project number:** 5R01GM146005-02
- **Recipient organization:** UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH
- **Principal Investigator:** ERIK M JORGENSEN
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $317,240
- **Award type:** 5
- **Project period:** 2023-02-01 → 2027-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10766800

## Citation

> US National Institutes of Health, RePORTER application 10766800, Genome engineering in the nematode C. elegans (5R01GM146005-02). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10766800. Licensed CC0.

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