# Functional Roles of Nascent RNA Structure in Regulating and Coordinating Gene Expression

> **NIH NIH R01** · NORTHWESTERN UNIVERSITY · 2020 · $297,032

## Abstract

SUMMARY
RNA structures can influence many aspects of gene expression including transcription, translation, splicing,
and polyadenylation. As RNA folding occurs immediately during transcription, this raises a fundamental
question as to how nascent RNA structures influence RNA processing and gene expression. Here we will
address aspects of this question through detailed structure-function studies of riboswitches, broadly distributed
regulatory RNAs that in response to binding specific ligands can control transcription, translation and splicing.
Riboswitches consist of two domains – a highly structured aptamer that can bind a specific ligand, and a
downstream expression platform that changes structure and regulates expression due to aptamer-ligand
interactions. Riboswitches sense an array of metabolites, metals, ions and other small molecules to regulate
essential and virulence genes in medically important pathogens such as Listeria monocytogenes,
Staphylococcus aureus and Vibrio cholerae, making them of great interest as targets for novel antimicrobial
therapies. They are also being developed as novel biosensors for biomedical applications. Riboswitches are
powerful model systems for understanding diverse areas of RNA biology including RNA-ligand interactions,
mechanisms of gene regulation, cellular RNA structures, and structure-based drug discovery. In addition, a
critical feature of many riboswitches is that regulation only occurs during transcription, making them ideal
model systems to study the impacts of nascent RNA structure on gene expression.
 Towards our long-term goal of developing a molecular understanding of how cotranscriptional RNA
folding regulates and coordinates gene expression and RNA processing, we are using diverse riboswitches
that regulate transcription as model systems. This proposal details a set of complementary specific aims that
address fundamental questions: (1) what are the sequence determinants and transcription dynamics that
promote efficient expression platform folding through cotranscriptional strand displacement, and (2) what are
the mechanisms by which aptamer-ligand interactions block cotranscriptional strand displacement to enact the
regulatory decision. To address these questions, we will apply a ‘function-first’ research strategy that uses
complementary approaches including FACS-seq to rapidly functionally characterize riboswitch sequence
variants in cells, cotranscriptional SHAPE-Seq (selective 2’-hydroxyl acylation analyzed by primer extension
sequencing) to characterize ligand-dependent cotranscriptional folding at nucleotide resolution, RNA
polymerase mutants to uncover the coupling of transcription dynamics to riboswitch folding and function, and
computational data analysis approaches to study the structure-function linkage in riboswitches. Detailed
knowledge of how cotranscriptional RNA folding links to nascent RNA-ligand interactions and gene regulation
will contribute to a deeper understanding of gene ...

## Key facts

- **NIH application ID:** 9888100
- **Project number:** 1R01GM130901-01A1
- **Recipient organization:** NORTHWESTERN UNIVERSITY
- **Principal Investigator:** Julius Beau Lucks
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $297,032
- **Award type:** 1
- **Project period:** 2020-01-01 → 2023-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9888100

## Citation

> US National Institutes of Health, RePORTER application 9888100, Functional Roles of Nascent RNA Structure in Regulating and Coordinating Gene Expression (1R01GM130901-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9888100. Licensed CC0.

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