Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Pseudouridine (Ψ) is the most abundant mRNA modification in mammals.
• Its functional roles are poorly understood due to challenges in transcriptome-wide mapping.

Purpose of the Study:

• To develop a method for quantitative, transcriptome-wide mapping of pseudouridine.
• To investigate the biological functions of pseudouridine modifications.

Main Methods:

• Developed a nanopore native RNA sequencing method for quantitative Ψ prediction (NanoPsu).
• Employed native content training, machine learning, and single-read linkage analysis.
• Applied NanoPsu to analyze interferon-stimulated gene transcripts.

Main Results:

• Successfully mapped pseudouridine modifications across the transcriptome.
• Identified interferon-inducible pseudouridine modifications in stimulated genes.
• Demonstrated the utility of NanoPsu for quantitative Ψ prediction.

Conclusions:

• Pseudouridine modifications are dynamically regulated by interferon stimulation.
• Pseudouridine plays a role in enhancing the efficacy of mRNA vaccines.