KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions

Area of Science:

• Molecular Biology
• Genomics
• Biochemistry

Background:

• RNA structure and interactions are crucial for cellular functions but remain poorly understood.
• The assembly of RNA and RNA-binding proteins into higher-order structures is largely unknown.
• Interactions between RNA molecules and their roles in facilitating functions require further investigation.

Purpose of the Study:

• To develop a novel method for detecting RNA-RNA interactions and higher-order RNA structures within cells.
• To investigate the impact of translation on mRNA structure.
• To explore viral-host RNA interactions and their potential role in viral replication.

Main Methods:

• KARR-seq utilizes N3-kethoxal labeling and multifunctional chemical crosslinkers.
• This technique covalently traps and determines RNA-RNA interactions and higher-order RNA structures.
• KARR-seq operates independently of local protein binding to RNA, ensuring RNA-centric analysis.

Main Results:

• KARR-seq accurately depicts higher-order RNA structures and detects widespread intermolecular RNA-RNA interactions.
• Translation was found to repress mRNA compaction under both native and stress conditions.
• The higher-order RNA structures of respiratory syncytial virus (RSV) and vesicular stomatitis virus (VSV) were determined.

Conclusions:

• KARR-seq is a sensitive and accurate method for studying RNA structures and interactions in vivo.
• Translation plays a significant role in regulating mRNA compaction.
• Identified viral-host RNA interactions may offer new insights into viral replication regulation.