# Revealing the dynamics of RNA metabolism with nucleotide recoding chemistry

> **NIH NIH R01** · YALE UNIVERSITY · 2020 · $360,956

## Abstract

PROJECT SUMMARY
Cellular RNA levels in both healthy and diseased cells are highly dynamic, yet most analyses of
RNA concentrations (RNA-sequencing, RNA-seq) capture only a static snapshot of cellular
RNA. RNA levels are controlled at diverse steps in RNA metabolism including transcriptional
initiation, transcriptional pausing, RNA processing, and RNA degradation. While RNA-seq
provides a global method to identify RNAs that are up or down-regulated in response to
biological perturbations, specialized experiments are required to determine which specific steps
of RNA metabolism are affected. The specialized nature of these experiments, however, limits
their wide-spread use. Thus, there is a pressing need to develop a flexible experimental
platform that can be easily adapted to study the kinetics of a broad range of the regulated steps
in RNA metabolism. The overall objective of this work is to add a temporal dimension to RNA-
seq, transforming it from a static endpoint assay into a robust technique to measure the kinetics
of RNA metabolism and reveal the diverse ways these kinetics are regulated and impacted by
disease. This platform is based on metabolic labeling and improvements in nucleotide chemistry
to study RNA dynamics at a range of timescales. The full potential of these approaches will be
realized once they are integrated a robust and unified platform to examine RNA metabolism
across a range of timescales (min to days), and transcript sizes (miRNA to long mRNA). Aim 1
is to determine optimal ways to globally distinguish changes in RNA synthesis from changes in
RNA stability. The statistical power of these experiments will be systematically examined to
define optimal experimental designs. Differences in RNA synthesis and degradation will be
measured in cell lacking an enzyme that promotes mRNA decapping in comparison with wild
type cells. The direct targets of this enzyme are expected to be post-transcriptionally stabilized
but unchanged transcriptionally. Aim 2 will extend this system to measure the dynamics of short
RNAs, including target directed miRNA degradation. Aim 3 includes the measurement the
transient RNA expression and RNA processing, and the integration of these approaches to
study the p53 tumor suppressor pathway. Successful completion of these aims will establish
nucleotide recoding chemistry as a general platform to reveal RNA dynamics across distinct
levels of gene expression.

## Key facts

- **NIH application ID:** 9943124
- **Project number:** 1R01GM137117-01
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Matthew David Simon
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $360,956
- **Award type:** 1
- **Project period:** 2020-07-01 → 2024-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9943124

## Citation

> US National Institutes of Health, RePORTER application 9943124, Revealing the dynamics of RNA metabolism with nucleotide recoding chemistry (1R01GM137117-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9943124. Licensed CC0.

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