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Ribosome Profiling

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Related Experiment Video

Updated: Jun 2, 2025

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

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Quantitative Proteomics Identifies Profilin-1 as a Pseudouridine-Binding Protein.

Songbo Wei¹, Xiaoxia Dai¹, Jun Yuan¹

¹Department of Chemistry, University of California, Riverside, California 92521-0403, United States.

Journal of the American Chemical Society

|January 15, 2025

Summary

Profilin-1 (PFN1) directly binds pseudouridine (Ψ)-containing RNA, revealing its role as a Ψ reader protein. This interaction is vital for regulating mRNA stability and translation, particularly for the TPI1 gene.

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Last Updated: Jun 2, 2025

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

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Published on: September 30, 2016

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Published on: February 17, 2023

Area of Science:

RNA biology
Molecular biology
Proteomics

Background:

Pseudouridine (Ψ) is the most abundant RNA modification, yet its biological functions remain largely unknown.
Understanding RNA modifications is crucial for deciphering gene regulation and cellular processes.

Purpose of the Study:

To identify proteins that bind to pseudouridine (Ψ) in RNA.
To investigate the functional role of the identified reader protein in post-transcriptional gene regulation.

Main Methods:

Unbiased quantitative proteomics to identify Ψ-binding proteins.
RNA-binding assays to confirm direct and selective binding of PFN1 to Ψ-containing RNA.
Analysis of PFN1 binding sites in human cells, including specific mRNA targets like TPI1.

Main Results:

Profilin-1 (PFN1) was identified as a direct and selective reader of Ψ-containing RNA.
Approximately 4000 PFN1 binding sites were mapped in human cells, including a known dyskerin (DKC1)-installed Ψ site in TPI1 mRNA.
PFN1 and DKC1 were found to be essential for regulating TPI1 mRNA stability and translation efficiency via PFN1-Ψ interaction.

Conclusions:

Profilin-1 (PFN1) is a novel reader protein for pseudouridine (Ψ) in RNA.
The PFN1-Ψ interaction plays a significant role in post-transcriptional regulation of gene expression.
This discovery sheds light on the functional importance of Ψ modifications and their impact on metabolic enzyme expression.