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Related Experiment Video

Updated: Aug 2, 2025

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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Transcriptome-wide identification of single-stranded RNA binding proteins.

Ruiqi Zhao1, Xin Fang1, Zhibiao Mai2

  • 1College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China xcweng@whu.edu.cn xzhou@whu.edu.cn.

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|April 17, 2023
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Summary

A new KASRIC method identifies single-stranded RNA binding proteins (ssRBPs) by combining RNA structure probing with protein profiling. This approach discovered 189 novel ssRBPs involved in RNA splicing and degradation.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • RNA secondary structures regulate crucial RNA-protein interactions in biological processes.
  • Identifying proteins that bind specific RNA structures is vital for understanding the RBPome.

Purpose of the Study:

  • To develop a novel strategy for the large-scale identification of single-stranded RNA binding proteins (ssRBPs).
  • To characterize the transcriptome-wide landscape of ssRBPs and their functions.

Main Methods:

  • Developed the Kethoxal Assisted Single-stranded RNA Interactome Capture (KASRIC) strategy.
  • Integrated RNA secondary structure probing with conventional RNA-binding protein profiling.
  • Applied KASRIC to HeLa cells for transcriptome-wide ssRBP identification.

Main Results:

  • Identified 3180 candidate RNA-binding proteins (RBPs) and 244 candidate ssRBPs.
  • Discovered 189 novel ssRBPs, in addition to 55 previously reported ones.
  • Functional analysis revealed ssRBPs are enriched in RNA splicing and degradation pathways.

Conclusions:

  • The KASRIC strategy enables efficient, transcriptome-wide identification of ssRBPs.
  • KASRIC significantly expands the known repertoire of ssRBPs and their functional roles.
  • This method will advance the study of RNA-protein interactions and the RBPome.