# Single cell analysis of dynamic gene regulation

> **NIH NIH R01** · VANDERBILT UNIVERSITY · 2022 · $363,946

## Abstract

PROJECT SUMMARY/ABSTRACT
Regulatory mechanisms underlying the precise control of gene expression in normal and disease states
involve multiprotein complexes such as the highly conserved Spt-Ada-Gcn5 Acetyltransferase (SAGA)
complex. Although most of the SAGA subunits have been identified, it remains essentially unknown how their
functions are coordinated to precisely regulate gene expression. Thus, the SAGA complex represents an ideal
paradigm to explore how multiprotein complexes regulate gene expression, and the overall goal of this project
is to provide a precise mechanistic and predictive understanding for the coordination of SAGA subunit function.
SAGA subunits are organized into “activity modules”. We will focus on the well-established histone
acetyltransferase (HAT), TATA-binding protein (TBP), and histone deubiquitinase (DUB) activity modules in
SAGA, which contain the best characterized and evolutionarily conserved SAGA subunits, and are implicated
in the regulation of chromatin structure (HAT), transcription initiation (TBP) and RNA export (DUB). Our central
hypothesis is that SAGA subunits and modules function together to precisely coordinate different steps in gene
expression from chromatin regulation to RNA transcription to RNA export. We will investigate osmotic stress
induction of high osmolarity glycerol (Hog1/p38) mitogen-activated protein kinase (MAPK) signaling and gene
expression in yeast to study SAGA subunit coordination of gene expression. Importantly, we will use a newly
developed detailed and integrated experimental and computational analysis of dynamic single-molecule RNA
expression (FISH) in single cells to simultaneously quantify and model each of these steps in gene regulation.
Excitingly, our preliminary studies have revealed that the histone acetyltransferase Gcn5p increases the
dynamics of chromatin states and stochasticity in gene expression but does not regulate basal transcription,
transcription initiation, or RNA degradation. We will determine how the specific HAT module subunits regulate
chromatin structure and the kinetics of these processes (Aim 1). We will elucidate how transcription initiation is
regulated by unique TBP module subunits (Aim 2). And we will reveal how the specific DUB module subunits
differentially regulate RNA export (Aim 3). To accomplish these aims, we propose a rigorous framework of
quantitative and dynamic single-cell experiments integrated with sophisticated data analysis and predictive
single-cell modeling. This innovative approach will mechanistically dissect gene regulation by the medically
relevant and evolutionary conserved multiprotein SAGA complex, providing the first comprehensive analysis of
multiprotein gene regulatory complex coordination of gene expression within a single experiment. Furthermore,
our studies will provide a blueprint to dissect how other multiprotein complexes regulate gene expression.

## Key facts

- **NIH application ID:** 10436385
- **Project number:** 5R01GM140240-02
- **Recipient organization:** VANDERBILT UNIVERSITY
- **Principal Investigator:** Gregor Neuert
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $363,946
- **Award type:** 5
- **Project period:** 2021-07-01 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10436385

## Citation

> US National Institutes of Health, RePORTER application 10436385, Single cell analysis of dynamic gene regulation (5R01GM140240-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10436385. Licensed CC0.

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