# Single-molecule visualization of transcription regulation mechanisms

> **NIH NIH R01** · BRANDEIS UNIVERSITY · 2024 · $434,647

## Abstract

Project Summary
The goal of this project is to contribute to understanding of the biochemical and biophysical mechanisms by
which gene expression is regulated. In particular, we seek to understand the operation of the molecular
machinery that regulates production of mRNA by DNA transcription and the relationship between the
composition and structures of the macromolecular complexes that make up that machinery and their
functions.
In this project, we have developed and applied a powerful approach to quantitatively defining the dynamic
molecular mechanisms of transcription and transcription regulation in vitro. Instead of studying populations
of molecules, we use multi-wavelength single-molecule fluorescence methods to directly visualize in vitro
the RNA polymerase and associating regulatory proteins simultaneously on hundreds of isolated individual
DNA molecules in multiplex. We propose continuing studies that apply this approach to elucidating dynamic
molecular regulation mechanisms of the messenger RNA synthesis machinery from an example bacterium
(E. coli) and from a model eukaryote (the budding yeast S. cerevisiae). In both systems, we have chosen for
study transcription factors and regulatory activities that are general mechanisms which act during
transcription of many or most protein-coding genes in the organism. Our studies will advance the field by
focusing not on single regulatory factors in isolation but on understanding the emergent properties of
systems in which multiple regulatory factors act together.
Our immediate goals are to use multi-wavelength single-molecule fluorescence methods in vitro to 1) test
the hypothesis that bacterial RNA polymerase elongation complexes are specialized by alternative modes
of σ70 binding and determine how specialization dictates different combinatorial regulation by elongation
factors NusA and NusG; 2) reveal the mechanisms that determine the outcome of the bacterial post-
termination complex; and 3) define the pathways by which selected general elongation factors compete and
cooperate for recruitment to eukaryotic RNA polymerase II elongation complexes.

## Key facts

- **NIH application ID:** 10885598
- **Project number:** 2R01GM081648-17
- **Recipient organization:** BRANDEIS UNIVERSITY
- **Principal Investigator:** JEFF GELLES
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $434,647
- **Award type:** 2
- **Project period:** 2007-07-15 → 2028-02-29

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10885598

## Citation

> US National Institutes of Health, RePORTER application 10885598, Single-molecule visualization of transcription regulation mechanisms (2R01GM081648-17). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10885598. Licensed CC0.

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