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

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.