# Investigating UPF3 paralog function in Nonsense-Mediated mRNA Decay and Genetic Compensation

> **NIH NIH K99** · OHIO STATE UNIVERSITY · 2024 · $62,075

## Abstract

Abstract
Nonsense Mediated mRNA Decay (NMD) degrades both aberrant transcripts containing Premature Termination
Codons (PTCs) and “normal” transcripts with other specific features. Regulation by NMD is pervasive and
estimated to impact around 10% of the transcriptome. UPF3 is a central NMD factor that bridges the mRNA
bound Exon Junction Complex (EJC) with the rest of the NMD machinery and aids in PTC recognition. In
mammals, there are two paralogs of UPF3, UPF3A and UPF3B, that have been documented to have both distinct
biological roles and functions. We and others previously found that UPF3A can compensate for UPF3B in NMD,
but is a weaker activator; moreover, this difference in activity is conferred by the “mid” domain. Moreover,
overexpression of UPF3A, but not UPF3B stabilizes an NMD reporter mRNA. To understand the different
propensities of UPF3 paralogs to stimulate NMD, we performed immunoprecipitation followed by mass
spectrometry to identify their associated factors. In addition to EJC and NMD components, we identified
transcriptional regulators and nucleocytoplasmic shuttling factors to be among some of the most enriched factors
in UPF3A and UPF3B immunoprecipitation. We also identified members of the nuclear transcription regulating
Little/Super Elongation Complex (LEC/SEC); the LEC was previously identified as an NMD factor that promotes
UPF3B association with the EJC. UPF3 is a nucleocytoplasmic shuttling protein, but its nuclear functions are
unknown. For the K99 phase (Aim 1), I am investigating the impact of these nuclear functions on UPF3
deposition and NMD activity. I hypothesize that nuclear import is required for UPF3 function in NMD, and the
LEC/SEC mediate nuclear UPF3 deposition onto nascent mRNPs. I am also investigating the functional
differences between the UPF3 paralogs in human cells and in zebrafish development; I hypothesize that
differential nuclear deposition underlies some of the functional differences between UPF3A and UPF3B, and
their distinct roles in vivo arise from these functional, rather than expression differences. This supplement is to
help maintain research productivity of Aim 1 (K99 phase) of the parent grant after I return from maternity
leave to allow me to focus on key aspects of research training. In zebrafish, Upf3a was implicated in the
poorly characterized Genetic Compensation Response (GCR) via interaction with nuclear histone modifiers, and
we found that this interaction is conserved in human cells. For the R00 phase (Aim 2), I will characterize the
mechanism of GCR initiation from NMD-targeted mRNAs. This supplement will help facilitate a timely transition
to an independent position and the research proposed in Aim 2. Taken together, this work will deepen our
understanding of how events in the nucleus and cytoplasm are coordinated to regulate cytoplasmic mRNA decay
and its feedback to transcriptional regulation.

## Key facts

- **NIH application ID:** 11094240
- **Project number:** 3K99GM154061-01S1
- **Recipient organization:** OHIO STATE UNIVERSITY
- **Principal Investigator:** Rene Marlene Arvola
- **Activity code:** K99 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $62,075
- **Award type:** 3
- **Project period:** 2024-04-05 → 2026-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11094240

## Citation

> US National Institutes of Health, RePORTER application 11094240, Investigating UPF3 paralog function in Nonsense-Mediated mRNA Decay and Genetic Compensation (3K99GM154061-01S1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/11094240. Licensed CC0.

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