Reactivity-based RNA profiling for analyzing transcriptome interactions of small molecules in human cells

Area of Science:

• Biochemistry
• Molecular Biology
• Pharmacology

Background:

• Small-molecule drugs targeting proteins can unintentionally bind to intracellular RNA, leading to toxicity.
• There is a growing need for novel therapeutic strategies that intentionally target RNA molecules.

Purpose of the Study:

• To present a protocol for globally profiling RNA-drug interactions in human cells.
• To identify drug-binding RNA sites at single-nucleotide resolution.
• To reveal the extent of transcriptome interactions with drugs.

Main Methods:

• Utilizing acylating probes for target RNA labeling.
• Employing next-generation sequencing for high-throughput analysis.
• Developing bioinformatic pipelines for data interpretation.

Main Results:

• Successfully profiled RNA-drug interactions across approximately 16,000 poly(A)+ human transcripts.
• Achieved single-nucleotide resolution in identifying drug-binding RNA loci.
• Demonstrated a streamlined workflow for comprehensive transcriptome-wide interaction mapping.

Conclusions:

• The developed protocol offers a powerful tool for understanding RNA-drug interactions.
• This method can aid in predicting and mitigating drug toxicity.
• It facilitates the discovery and development of novel RNA-targeted therapeutics.