Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity

Area of Science:

• Molecular Biology
• Neuroscience
• Epigenetics

Background:

• Pseudouridine (psi) is a crucial mRNA modification influencing gene expression.
• Regulation of psi dynamics, particularly in neuronal cells, remains poorly understood.
• Understanding psi regulation is vital for comprehending neuronal function and disease.

Purpose of the Study:

• To investigate pseudouridine dynamics in neuronal cells under different conditions.
• To explore the impact of retinoic acid differentiation and lead exposure on psi modifications.
• To identify regulatory mechanisms controlling psi in neurons.

Main Methods:

• Nanopore direct RNA sequencing was employed to profile psi modifications.
• SH-SY5Y cells were used to model healthy (differentiation) and unhealthy (lead exposure) cellular states.
• Quantitative analysis of psi site occupancy and writer expression was performed.

Main Results:

• Significant changes in psi writer expression were observed during physiological conditions.
• Lead-treated cells exhibited increased psi sites but reduced relative psi occupancy.
• Highly plastic psi sites were found with constant writer expression, suggesting trans-regulation.
• Static psi modification sites indicated a potential "housekeeping" role.

Conclusions:

• This study provides novel insights into the regulation of mRNA pseudouridylation in neurons.
• Findings highlight the dynamic nature of psi modifications in response to cellular stress and differentiation.
• The research opens avenues for exploring psi's role in neuronal health and neuroprotection.