# Uncovering the regulatory principles of dynamic mRNA methylation

> **NIH NIH R35** · YALE UNIVERSITY · 2022 · $401,875

## Abstract

Project Summary
Chemical modiﬁcation of RNA is a critical mechanism of gene expression regulation, controlling RNA
processing, stability, and, in the case of mRNA, translation. The chemical diversity of RNA modiﬁcations
suggests that there is extensive biology yet to be uncovered. A recent surge in this ﬁeld has been driven largely
by rapid advances in high throughput sequencing methods that allow us to map these marks on a
transcriptome-wide scale. However, the majority of studies remain correlative and are not able to reveal the
molecular mechanisms of RNA modiﬁcation function or regulation. The information we glean from such studies
often represents an average across all transcripts in the cell, and does not take into account the spatial
organization or temporal control of RNA transcription, processing, and trafﬁcking. Moreover, the majority of
work on mRNA modiﬁcations has focused on a single modiﬁcation, N6-methyladenosine (m6A), which
represents only one of over one hundred modiﬁcations annotated to date. Here we describe two research
directions in our laboratory that address fundamental questions about mRNA modiﬁcations. The ﬁrst research
direction aims to characterize a new mRNA modiﬁcation, N1-methyladenosine (m1A). Since discovering this
modiﬁcation in mRNA in during my postdoctoral work, technical challenges have prevented us from
understanding the functions and regulation of this mRNA modiﬁcation. These challenges have also led to
conﬂicting data and controversy over the presence and prevalence of m1A in mRNA. We have recently
validated new m1A mRNA sites and we are now well positioned to ﬁnally shed light on this mysterious mRNA
modiﬁcation. The second research direction aims to identify the mechanisms that coordinate cotranscriptional
modiﬁcation of mRNAs as they are being synthesized. This remains mysterious for even the most well-
characterized mRNA modiﬁcation, m6A. We hypothesize that RNA polymerase II complexes recruit RNA
modiﬁcation enzymes during transcription, akin to how splicing and processing factors are cotranscriptionally
recruited to nascent mRNA. Using detailed biochemistry and RNA labeling approaches, we will dissect the
mechanisms of cotranscriptional RNA methylation. To tackle challenges such as these, our lab identiﬁes
speciﬁc settings, essentially molecular model systems, that allow us to dissect the molecular mechanisms of
RNA modiﬁcation-mediated regulation of gene expression. Once we reveal the regulatory components and
principles that govern these speciﬁc systems, we then have a molecular foothold to determine how general or
speciﬁc these principles are, and in which contexts they apply. Our work will open up a new areas of RNA
biology and allow us to understand how defects in these mechanisms result in associated human diseases.

## Key facts

- **NIH application ID:** 10498323
- **Project number:** 1R35GM146919-01
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Sigrid H Nachtergaele
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $401,875
- **Award type:** 1
- **Project period:** 2022-08-01 → 2027-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10498323

## Citation

> US National Institutes of Health, RePORTER application 10498323, Uncovering the regulatory principles of dynamic mRNA methylation (1R35GM146919-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10498323. Licensed CC0.

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