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

Protein-targeted small-molecule drugs may unintentionally bind intracellular RNA, contributing to drug toxicity. Moreover, new drugs are actively sought for intentionally targeting RNA. Here, we present a protocol to globally profile RNA- drug interactions in human cells using acylating probes and next-generation sequencing. We describe steps for cell culture, target acylation, library preparation, and sequencing. Detailed bioinformatic analyses identify drug-binding RNA loci in similar to 16,000 poly(A)+ human transcripts. This streamlined workflow identifies RNA- drug interactions at single- nucleotide resolution, revealing widespread transcriptome interactions of drugs. For complete details on the use and execution of this protocol, please refer to Fang et al.(1)