# Characterizing epistasis in yeast using CRISPR and chromosome synthesis

> **NIH NIH R35** · UNIVERSITY OF SOUTHERN CALIFORNIA · 2024 · $445,705

## Abstract

Project Summary
The long-term goal of this research program is to understand how genetic interaction among loci
(or ‘epistasis’) contributes to phenotypic variation. To achieve this objective, we will pursue two
parallel research trajectories. First, we will continue our ongoing work to characterize the
genetic and molecular mechanisms that cause spontaneous and induced mutations to show
different effects across genetically distinct individuals. These ‘background effects’ are important
to human health because they complicate efforts to predict, prevent, and treat disease based on
personalized genomic data. We recently used combinatorial DNA barcoding and CRISPR
interference (‘CRISPRi’) to screen thousands of protein-coding genes in yeast for background
effects in 170 progeny from a cross. With these data, we identified 815 background effects,
quantified how background effects shape the phenotypic variance in populations, and mapped a
subset of loci causing these background effects. Here, we will extend our work by
comprehensively dissecting the genetic bases of hundreds of these already identified
background effects, examining the environmental contextuality of these background effects, and
determining how certain ‘hotspot’ loci shape the effects of many different genetic perturbations.
Second, we have developed an approach for cloning segments of natural chromosomes and
assembling them into synthetic chromosomes that can replace the native chromosomes in cells.
This method opens new opportunities for characterizing epistasis without a need for mating or
meiosis. As proof-of-principle, we showed that a single chromosome could explain nearly the
entire difference in the abilities of two yeast species to grow at high temperature. Half of this
effect was due to epistasis between different chromosomal segments. Here, we will improve the
scalability, versatility, and portability of our technique, and will use it to determine how epistasis
shapes trait differences and isolation between yeast species and genera. Our two research
directions will produce detailed insights into epistasis that advance efforts to understand and
predict the relationship between genotype and phenotype.

## Key facts

- **NIH application ID:** 10763341
- **Project number:** 2R35GM130381-06
- **Recipient organization:** UNIVERSITY OF SOUTHERN CALIFORNIA
- **Principal Investigator:** Ian Michael Ehrenreich
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $445,705
- **Award type:** 2
- **Project period:** 2019-01-01 → 2029-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10763341

## Citation

> US National Institutes of Health, RePORTER application 10763341, Characterizing epistasis in yeast using CRISPR and chromosome synthesis (2R35GM130381-06). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10763341. Licensed CC0.

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