# Mechanisms and Phenotypic Consequences of Structural Genomic Variation

> **NIH NIH R35** · COLORADO STATE UNIVERSITY · 2023 · $55,757

## Abstract

Argueso Lab – PA-20-272 – Administrative Supplement to Existing Grants and Cooperative
Agreements
NIH Project Summary/Abstract:
 One of the copy number variation (CNV) mechanisms that we are investigating is de novo recurrent
CNVs. These result in duplications and deletions in offspring that are not seen in parents. Furthermore,
the same genetic breakpoints are seen in unrelated individuals. Non-allelic homologous recombination
(NAHR) during meiosis, mediated by low copy repeat (LCR) regions in the genome causes these
rearrangements. This is an important mechanism to study because some forms of autism and other
neurodevelopmental disorders in humans are associated with recurrent CNVs, and about 5-10% of the
human genome is made up of low copy repeats. The potential for these genome rearrangements exists
in normal, healthy people. We are interested in finding the factors that modulate the frequency of
recurrent CNVs using Saccharomyces cerevisiae as our detection system.
 In our parent award, we described an assay system in yeast to study this phenomenon and to
positively detect the CNVs in resulting haploid spores. We did this by placing a CNV reporter system,
which uses the genes SFA1 and CUP1, and drug resistance markers in between engineered LCRs. We can
identify CNVs with this original system via the standard method of tetrad dissections, which is a tried-
and-true method to follow the segregation of markers after meiosis but is slow and laborious. We have
modified our original assay system to also include spore autonomous fluorescence markers in between
our engineered LCRs. With our new fluorescence system, we can assess hundreds of tetrads in a matter
of hours, whereas with tetrad dissections we can assess 100-200 tetrads in about a week.
 To image our cells, we need to: 1) see them using brightfield microscopy, and 2) use fluorescence
microscopy to determine which of the four spores are glowing red or green. We have tested our strains
with a fluorescence microscope that belongs to a neighbor lab in our department, and the assay system
works beautifully. This is a great microscope, but it poses a couple of problems for us: 1) It is in high
demand and we do not have priority access to it, so it is challenging to get time on it. This will severely
limit our ability to drive our investigation of recurrent CNVs forward. 2) This microscope is much more
capable than we need and is not appropriately set up to image yeast cells because it lacks phase
contrast. We are proposing to purchase a simpler and more affordable fluorescence microscope that
has appropriate specifications to meet our needs. This new microscope will enable us to efficiently
assess recurrent CNVs and to expand our experiments to study the architecture of LCRs and to include
more mutants in our investigation of the genetic control of recurrent CNV formation.

## Key facts

- **NIH application ID:** 10797221
- **Project number:** 3R35GM119788-08S1
- **Recipient organization:** COLORADO STATE UNIVERSITY
- **Principal Investigator:** Juan Lucas Argueso
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $55,757
- **Award type:** 3
- **Project period:** 2016-08-11 → 2026-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10797221

## Citation

> US National Institutes of Health, RePORTER application 10797221, Mechanisms and Phenotypic Consequences of Structural Genomic Variation (3R35GM119788-08S1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10797221. Licensed CC0.

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