RNA modifications in structure prediction - Status quo and future challenges.

Area of Science:

• Molecular Biology
• Bioinformatics
• Genetics

Background:

• Chemical modifications of RNA nucleotides alter genetic and structural information.
• Transfer RNA (tRNA) and ribosomal RNA (rRNA) are heavily modified, crucial for their functional structures.
• Recent RNomics studies reveal widespread RNA modifications across the transcriptome, termed the epitranscriptome.

Purpose of the Study:

• To review RNA modifications and their associated structures from a computational perspective.
• To discuss substrate structures, their properties, and the impact of modifications on RNA folding.
• To evaluate the applicability of existing RNA structure prediction methods for studying epitranscriptomic effects.

Main Methods:

• Review of existing literature on RNA modifications and computational structure prediction.
• Analysis of substrate structures and their properties, including sub-motifs.
• Examination of how modifications influence base pairing and refolding events.

Main Results:

• RNA modifications require specific substrate structures that influence folding and refolding.
• Modifications can stabilize or destabilize RNA structures, affecting regulatory functions.
• Established RNA structure prediction methods may need adaptation to incorporate modified nucleotides.

Conclusions:

• Computational approaches are essential for understanding the epitranscriptome's role in RNA structure and regulation.
• Further development of prediction methods is needed to accurately model epitranscriptomic effects.
• Understanding RNA modifications is key to deciphering gene regulation and RNA function.