Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• RNA binding proteins (RBPs) are crucial for post-transcriptional gene regulation.
• Understanding RBP-RNA interactions is key to deciphering gene expression control.
• Protein-associated RNA-RNA interactions add complexity to gene regulation.

Purpose of the Study:

• To review recent advancements in CLIP-based methods for mapping RBP-RNA interactions.
• To focus on techniques enabling the profiling of protein-associated RNA-RNA interactions.
• To provide a framework for researchers studying RBP-associated RNA interactions.

Main Methods:

• Crosslinking and immunoprecipitation (CLIP) and its variants.
• Techniques for globally profiling protein-associated RNA-RNA interactions.
• Analysis of challenges and solutions in mapping complex RNA interactions.

Main Results:

• CLIP methods have been significantly improved for mapping RBP-RNA interactions.
• New techniques specifically address the profiling of protein-associated RNA-RNA interactions.
• Current approaches offer solutions to challenges in mapping these complex interactions.

Conclusions:

• Recent CLIP method improvements enhance the mapping of RBP-RNA interactions.
• Specialized techniques are emerging to profile intricate protein-associated RNA-RNA networks.
• This review provides a practical guide for investigating RBP-associated RNA interactions.