# Effects of Chromosomal Topology and Organization on E. coli Gene Expression

> **NIH NIH F31** · JOHNS HOPKINS UNIVERSITY · 2022 · $46,752

## Abstract

Project Summary/Abstract
 Bacterial chromosomes are organized spatially and topologically within cells, taking on conformations
that change as a function of cellular processes, growth rates and conditions external to the cell. Nucleoid-
associated proteins facilitate this organization by bending, looping, and coating DNA to form topological
domains at different length levels. At the lowest level, the E. coli chromosome forms small looping domains, or
chromosomal topologically isolated domains (TIDs), on the order of 10 kbp. This chromosomal organization
into topologically isolated domains localizes supercoiling to different portions of the chromosome. The
relationship between this and transcription is one of coupling, where supercoiling density determines
transcriptional activity, but transcriptional activity also changes supercoiling density. To probe these effects and
to test our hypothesis that the formation of TIDs significantly modulates gene expression profiles we will use a
combined single-molecule imaging and computational modeling approach.
 To learn the most about the DNA topological effects on transcription as we must be able to isolate the
various components in a series of synthetic systems. In Aim 1, I will construct an in vivo synthetic looping
domain to investigate the effect of domain formation on the transcription and expression dynamics of two
genes inside the domain under different conditions. Expression will be monitored via single molecule
fluorescence in situ hybridization and live protein expression from synthetic looping domains. In Aim 2, to
obtain a quantitative understanding of how the topological state of a TID impacts RNAP’s transcription kinetics,
I will monitor the initiation and elongation rates of single RNAP molecules on a circular template DNA
mimicking a TID using single molecule protein induced fluorescent enhancement (smPIFE) in vitro. In Aim 3,
to synthesize the models at these two size scales by using a reaction-diffusion model to simulate DNA-protein
interactions and supercoiling. Studying bacterial chromosomal organization in this way may reveal
mechanisms that bacteria use to maintain transcription in the presence of perturbations and ways they may
exploit DNA topology effects for gene regulation.

## Key facts

- **NIH application ID:** 10465658
- **Project number:** 1F31GM146442-01
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Nicolas Naguib Yehya
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $46,752
- **Award type:** 1
- **Project period:** 2022-09-30 → 2024-09-29

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10465658

## Citation

> US National Institutes of Health, RePORTER application 10465658, Effects of Chromosomal Topology and Organization on E. coli Gene Expression (1F31GM146442-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10465658. Licensed CC0.

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