# Determining how noisy gene expression controls stochastic fate choices during development

> **NIH NIH F31** · JOHNS HOPKINS UNIVERSITY · 2021 · $46,036

## Abstract

Cell fate specification during development is often thought of as a highly reproducible process driven by
cell lineage and signaling. Cellular diversity can also arise from the inherent molecular noise (i.e. variability) in
gene expression during stochastic cell fate specification, where a cell randomly chooses between two or more
fates. Compared to lineage and signaling mechanisms, very little is known about how noise in gene expression
drives fate decisions during development.
 This project aims to address stochastic cell fate specification in the visual system of Drosophila
melanogaster. The fly eye contains a simple, stochastic, binary fate choice. The eye is a random mosaic of two
color-detecting photoreceptor subtypes, defined by expression of different light-detecting Rhodopsin proteins.
This binary decision is controlled by the transcription factor Spineless (Ss), which is expressed in a random
subset (65%) of R7 photoreceptors. Stochastic expression of the gene spineless (ss) is controlled in a
temporal manner throughout development by two enhancer elements (“early” and “late” enhancers), and a
transcriptional repressor, Klu. Early expression of ss is noisy, producing variability in the levels of gene
expression between precursor R7 cells. By manipulating DNA elements (enhancers and silencers) and the Klu
transcription factor, the strength of ss expression early can be tuned. Remarkably, these manipulations of early
expression cause changes in the on/off ratio of Ss in terminally differentiated R7 cells. Based on these
findings, it is hypothesized that variable levels of ss expression amongst R7 progenitors (i.e. early) sets the
on/off expression frequency in terminally differentiated R7 cells (i.e. late). This project aims to address what
promotes early ss expression variability as well as the consequences of this variability.
 A major source of gene expression noise arises from the process of transcription. Transcription is
inherently stochastic, and occurs in bursts that vary in amplitude, frequency, and duration between genes and
cells. Three-color RNA fluorescence in situ hybridization will be used to monitor transcription in individual cells
to determine how Klu and different DNA elements control variation in in early ss expression in fixed tissue (Aim
1). To gain a mechanistic understanding of how transcriptional affects early expression variability, this project
aims to visualize early ss expression by using the MS2/MCP system and live imaging (Aim 1). Finally, a link
between early expression and terminal cell fate will be made by monitoring endogenous ss expression in real
time from the precursor cell stage through terminal differentiation (Aim 2). This project will be carried out at
Johns Hopkins University in the lab of Robert J. Johnston Jr. The applicant will receive additional training from
collaborators at Princeton University and the Institut Pasteur (Dr. Thomas Gregor). The results of this project
will elucidate the mech...

## Key facts

- **NIH application ID:** 10241950
- **Project number:** 5F31EY031963-02
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Elizabeth Urban
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $46,036
- **Award type:** 5
- **Project period:** 2020-08-16 → 2022-08-15

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10241950

## Citation

> US National Institutes of Health, RePORTER application 10241950, Determining how noisy gene expression controls stochastic fate choices during development (5F31EY031963-02). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/10241950. Licensed CC0.

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