# Investigating the role of the Ccr4-Not complex in regulating codon optimality-mediated mRNA decay

> **NIH NIH F31** · JOHNS HOPKINS UNIVERSITY · 2024 · $48,974

## Abstract

PROJECT SUMMARY
The Ccr4-Not complex is the major regulator of codon optimality-mediated messenger RNA decay, a
mechanism that is intimately tied to translation rate. The disruption of co-translational mRNA decay events can
have major physiological effects, leading to haploinsufficiency or contributing to cancer. For instance, CNOT3,
a subunit of the Ccr4-Not complex, was recently identified as a tumor suppressor that is mutated in 7.9% of
adult T-cell acute lymphoblastic leukemias (T-ALLs). Recent work in our lab identified that Not5 (yeast
homolog of human CNOT3) directly binds to the E-site of slowly translating ribosomes, leading to the
preferential decay of non-optimal mRNA transcripts. This interaction was recently found to be conserved in
humans, suggesting a mechanism for how cells use the mRNA decay machinery to alter transcript levels.
Though the structure of Not5 interacting with elongating ribosomes has been resolved, nothing is currently
known about how Not5 interacts with members of the Ccr4-Not complex to facilitate mRNA decay. Thus,
teasing apart how the decay machinery mechanistically regulates the degradation of mRNA will be critical in
understanding how cells regulate transcript levels as well as open avenues of therapeutic intervention for a
broad range of haploinsufficiency diseases and cancer. To address this gap in knowledge, I will
mechanistically dissect how the Ccr4-Not complex assembles onto actively translating ribosomes and assess
how the subunits of this complex coordinate the removal of the poly-A tail and 5’-cap of mRNAs using the
budding yeast, Saccharomyces cerevisiae as a model system. Preliminary data from our lab shows that Not5
binding to the ribosomal E-site is necessary for the recruitment of the mRNA decay factor, Dhh1, to translating
ribosomes, but the details of this recruitment pathway remain opaque. We do not yet understand if Not5 is
involved in the recruitment of the remaining mRNA decay factors and how this recruitment might coordinate
decay events. Likewise, the loss Dhh1 is known to exhibit decapping defects and recently we found that the
loss of this factor also exhibits defects in pol-A tail removal of mRNAs, meaning Dhh1 recruitment may serve to
bridge these 3’-5’ decay events. I hypothesize that Not5 recruits the remaining Ccr4-Not subunits to
actively translating ribosomes resulting in the timely decay of mRNA transcripts. I will address this
hypothesis through the following specific aims: Aim 1) I will systematically determine the assembly of the Ccr4-
Not complex subunits onto the translating mRNP structure and determine if this assembly is Not5-
dependent. Aim 2) I will characterize the contacts between Dhh1 and the Ccr4-Not complex to determine if
their interaction mediates the 3’-5’ communication of mRNA decay. The proposed studies will enhance our
mechanistic insight into how mRNA half-lives are regulated and provide the basis for detailed understanding of
this role in human disease.

## Key facts

- **NIH application ID:** 10899510
- **Project number:** 5F31GM151817-02
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Lana Nicole Christensen
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $48,974
- **Award type:** 5
- **Project period:** 2023-08-01 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10899510

## Citation

> US National Institutes of Health, RePORTER application 10899510, Investigating the role of the Ccr4-Not complex in regulating codon optimality-mediated mRNA decay (5F31GM151817-02). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10899510. Licensed CC0.

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