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Updated: May 5, 2026
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
Published on: July 3, 2010
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Protocol for transcriptome-wide mapping of small-molecule RNA-binding sites in live cells
Yuquan Tong1, Patrick R A Zanon2, Xueyi Yang1
1The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Department of Chemistry, 130 Scripps Way, Jupiter, FL 33458, USA; The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, FL 33458, USA.
STAR Protocols
|August 21, 2024
Summary
This study introduces a new protocol to map how small molecules interact with RNA in cells and in vitro. This method helps identify potential drug candidates by visualizing their molecular fingerprints on RNA.
Area of Science:
- Biochemistry
- Molecular Biology
- Chemical Biology
Background:
- Small molecules interacting with RNA are crucial as chemical probes and potential therapeutics.
- Detecting these interactions is challenging due to low affinity and short residence times.
Purpose of the Study:
- To present a protocol for mapping small molecule-RNA interactions.
- To enable visualization of molecular fingerprints across the human transcriptome in live cells.
Main Methods:
- The protocol involves compound treatment, cross-linking, and RNA extraction.
- RNA fragmentation, pull-down, RNA sequencing, and data analysis are detailed.
- This method allows for in vitro and in vivo analysis.
Main Results:
- The study provides a comprehensive protocol for mapping small molecule-RNA interactions.
- The described methods facilitate the identification of RNA-binding small molecules.
- This technique aids in understanding molecular interactions within the transcriptome.
Conclusions:
- The developed protocol offers a robust method for studying small molecule-RNA interactions.
- This technique can accelerate the discovery of novel RNA-targeting therapeutics.
- The protocol is applicable for both in vitro and cellular studies.
