Probing RNA structure in vivo.

Area of Science:

• Molecular Biology
• Biochemistry
• Genomics

Background:

• RNA structure is crucial for diverse biological functions.
• Understanding RNA structure in vivo is essential for deciphering its roles.
• Previous methods for RNA structure probing were limited in scope and application.

Purpose of the Study:

• To review recent advancements in chemical reagents and techniques for probing RNA structure in living cells.
• To highlight the capabilities of new genome-wide methods for RNA structurome analysis.
• To discuss the application of these techniques in elucidating RNA secondary and tertiary structures in vivo.

Main Methods:

• High-throughput, genome-wide techniques like Structure-seq2 and DMS-MaPseq utilize dimethylsulfate (DMS) for nucleobase modification.
• New chemical reagents including 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), glyoxal, and nicotinoyl azide (NAz) expand probing capabilities.
• Selective 2'-hydroxyl acylation and primer extension (SHAPE) reagents target ribose for detecting RNA flexibility.
• Psoralen analysis of RNA interactions and structures (PARIS) is used for crosslinking nucleobases.

Main Results:

• These techniques provide comprehensive, genome-wide RNA structuromes.
• The methods are applicable across various life domains and experimental conditions.
• New reagents significantly enhance the ability to probe nucleobases and RNA flexibility in vivo.

Conclusions:

• Emerging chemical reagents and high-throughput techniques offer powerful tools for in vivo RNA structure determination.
• These diverse methods enable detailed elucidation of RNA secondary and tertiary structures at a genome-wide scale.
• Advancements in RNA structure probing are critical for understanding gene regulation and cellular processes.