# Transcriptome Analysis with RNA-Reactive Probes

> **NIH NIH R35** · STANFORD UNIVERSITY · 2024 · $12,184

## Abstract

Summary of parent project (R35 GM145357)
Work in the last decade from many labs has underlined the critical importance of RNA-mediated
cellular pathways, and clear connections of specific RNAs to human health. RNAs are
increasingly viewed both as appealing therapeutic targets, and as therapeutic agents
themselves. We hypothesize that obtaining a deeper and broader understanding about how
ligands interact with the many RNA species of the cell will provide important new insights into
RNA networks and functions, provide new understanding of how current drugs cause cellular
toxicity, and lend novel insights into improving RNA therapies. We are convinced that the
analysis of RNA interactions transcriptome-wide is essential to future biomedicine.
Unfortunately, methods for assessing RNA interactions directly in the cell lag well behind those
for protein and proteome analysis.
This project will consolidate our RNA work into a broad program that will develop a new set of
RNA-reactive reagents and methods, and will apply them to provide specific, quantitative
information about ligand interactions with the transcriptome. We will develop first-in-class
methods for functionalizing native RNAs at specific sites, and novel strategies for controlling
RNAs with red light. Combining our reactive acyl tools and methods with next-gen sequencing,
we will pinpoint and quantify ligand binding sites in the whole transcriptome. These
methodologies, together termed Reactivity-Based RNA Profiling (RBRP), will be applied to
analyzing off-target RNA binding by known small-molecule drugs with clinically limiting toxicity,
to profiling RNA interactions of endogenous secondary metabolites, and to the analysis of how
modified bases in next-generation mRNA vaccines and therapeutics affect their structures and
interactions in the cell. This work is significant because it seeks answers to system-wide
clinically-relevant questions regarding RNA interactions. Further, it develops the 2’-OH group as
a nearly universal handle for manipulation, conjugation, and study of RNAs, introducing
enabling molecular technologies that will broadly benefit researchers in the fields of RNA
biology and contribute to improving future RNA therapies.

## Key facts

- **NIH application ID:** 11096997
- **Project number:** 3R35GM145357-03S1
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** ERIC T. KOOL
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $12,184
- **Award type:** 3
- **Project period:** 2022-05-01 → 2027-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11096997

## Citation

> US National Institutes of Health, RePORTER application 11096997, Transcriptome Analysis with RNA-Reactive Probes (3R35GM145357-03S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/11096997. Licensed CC0.

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