Nuclear 2'-O-methylation regulates RNA splicing through its binding protein FUBP1

Area of Science:

• Molecular Biology
• RNA Biology
• Epigenetics

Background:

• 2 -O-methylation (Nm) is a prevalent RNA modification in mammals, yet its protein recognition and nuclear functions remain largely unexplored.
• Understanding how proteins interact with Nm-modified RNA is critical for deciphering its regulatory roles.

Purpose of the Study:

• To identify proteins that bind to 2 -O-methylation (Nm) modified RNA.
• To investigate the functional significance of Nm-binding proteins in nuclear processes, particularly RNA splicing.

Main Methods:

• RNA affinity purification coupled with mass spectrometry to identify Nm-binding proteins.
• Electrophoretic mobility shift assays (EMSA) to validate protein-RNA interactions.
• Profiling of Nm sites in chromatin-associated RNA (caRNA) and analysis of FUBP1 occupancy.

Main Results:

• Identified several Nm-binding protein candidates, including the splicing factor FUBP1, which showed preferential binding to Nm-modified RNA.
• Nm modifications are enriched in intronic regions of caRNA and overlap with FUBP1-binding sites.
• Depletion of Nm led to exon skipping and reduced FUBP1 occupancy, while FUBP1 depletion induced exon skipping in Nm-modified genes.

Conclusions:

• FUBP1 is a novel Nm-binding protein that plays a significant role in RNA splicing regulation.
• RNA 2 -O-methylation (Nm) modification has previously unrecognized nuclear functions in mediating splicing regulation via proteins like FUBP1.