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

RNA structures are essential building blocks of functional RNA molecules. Profiling secondary structures in vivo and in real time remains challenging because RNAs exhibit dynamic structures and complex conformations. Besides the canonical stem-loop secondary structure, non-canonical structure RNA G-quadruplex (rG4) has attracted interest for its potential as a drug target. Early studies have demonstrated that RNAs can form distinct secondary structures. However, how distinct RNA structures, formed from the same RNA sequences, function within the transcriptome is poorly understood, and factors driving and regulating structure transitions remain to be investigated. Inspired by an HOXB9 segment able to form multiple structures, we found that many RNA segments across the transcriptome exhibit multi-faceted structure-forming potential. In the case of HOXB9, we demonstrate that N6-methyladenosine (m6A) modification influences RNA structure and binding to RNA-binding proteins (RBPs). Therefore, we collected RNA modification sites naturally occurring within the putative G-quadruplex-forming sequences (PQSs) of transcripts and developed MoRNiNG, a database for RNA modifications in natural rG4. MoRNiNG is structured with reliability tiers determined by the resolution of RNA modification sites and is designed to accommodate various large datasets. We experimentally validated the influence of m6A, 5-methylcytosine (m5C), and adenosine to inosine (A-to-I) editing on rG4-forming sequences, providing evidence to support the modification switch concept. The diversity and transition of secondary structures from the same RNA segment offer valuable insights into the regulation of RNA structure dynamics. MoRNiNG is freely accessible at https://www.cityu.edu.hk/bms/morning.