Transcript architecture predetermines m6A remodeling and sensory neuron vulnerability in chemotherapy-induced...

Area of Science:

• Molecular Biology
• Epigenetics
• Neuroscience

Background:

• The response of individual RNA transcripts to cellular perturbations is not fully understood.
• N6-methyladenosine (m6A) is a key epitranscriptomic modification influencing RNA fate.
• Bortezomib, a proteasome inhibitor, induces peripheral neuropathy and alters RNA profiles.

Purpose of the Study:

• To investigate whether intrinsic transcript features predetermine the response to drug-induced perturbations.
• To simultaneously profile m6A modifications, poly(A) tail dynamics, and full-length RNA isoforms.
• To understand the epitranscriptomic basis of bortezomib-induced neuropathy.

Main Methods:

• Nanopore direct RNA sequencing in male mouse dorsal root ganglia (DRG).
• Machine learning models to predict m6A loss based on transcript features.
• Unsupervised clustering to identify RNA response programs.
• Integration with single-nuclei sequencing data.

Main Results:

• Transcript-intrinsic features, not expression level, predetermined perturbation-induced m6A loss (R² = 0.983).
• Bortezomib removed a fixed fraction of m6A marks, with loss scaling linearly with baseline density.
• Identified four response programs, with m6A erosion linked to oxidative phosphorylation (OXPHOS) and proteasome genes.
• Sensory neurons exhibited a 2.2-fold greater m6A loss burden compared to non-neuronal cells.

Conclusions:

• Epitranscriptomic response to bortezomib is predetermined by RNA transcript architecture.
• Pathway specificity and cell-type vulnerability (e.g., sensory neurons) are downstream consequences of intrinsic RNA structure.
• Findings reveal a deterministic role of RNA architecture in cellular response to drug treatment.