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

ABSTRACT: 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 ∼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.

SUBMITTER: Fang L

PROVIDER: S-EPMC10643522 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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

Fang Linglan L Kool Eric T ET

STAR protocols 20231031 4

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 ∼16,000 poly(A)+ ...[more]

PMID: 37917579

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