MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics.

Area of Science:

• Molecular Biology
• Genomics
• RNA Biology

Background:

• RNA molecules exhibit dynamic secondary structures beyond canonical stem-loops, including G-quadruplexes (rG4s).
• Understanding how sequence-identical RNAs adopt different structures and how these transitions are regulated is crucial for deciphering transcriptome function.
• RNA modifications are increasingly recognized as key regulators of RNA structure and function.

Purpose of the Study:

• To investigate the influence of RNA modifications on the formation and transition of RNA secondary structures, particularly rG4s.
• To identify RNA segments with multi-faceted structure-forming potential across the transcriptome.
• To develop a comprehensive database of RNA modifications within natural rG4 sequences.

Main Methods:

• Bioinformatic analysis to identify putative G-quadruplex-forming sequences (PQSs) and associated RNA modification sites.
• Development of the MoRNiNG database, incorporating reliability tiers for modification site resolution.
• Experimental validation of the impact of N6-methyladenosine (m6A), 5-methylcytosine (m5C), and adenosine to inosine (A-to-I) editing on rG4 formation.

Main Results:

• Many RNA segments across the transcriptome possess the potential to form multiple distinct structures.
• N6-methyladenosine (m6A) modification was shown to influence HOXB9 RNA structure and RNA-binding protein (RBP) interactions.
• Experimental validation confirmed that m6A, m5C, and A-to-I editing can act as 'modification switches' regulating rG4 formation.

Conclusions:

• The diversity and dynamic transitions of RNA structures from the same sequence play a significant role in RNA regulation.
• RNA modifications are critical regulators of RNA structure, influencing G-quadruplex formation and potentially other structural conformations.
• The MoRNiNG database provides a valuable resource for studying RNA modifications in natural rG4s and advancing our understanding of RNA structure dynamics.