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

Pseudouridine (Ψ) is the most abundant RNA modification in nature; however, not much is known about the biological functions of this modified nucleoside. Employing an unbiased quantitative proteomics method, we identified multiple candidate reader proteins of Ψ in RNA, including a cytoskeletal protein profilin-1 (PFN1). We demonstrated that PFN1 binds directly and selectively to Ψ-containing RNA. Additionally, we discovered approximately 4000 binding sites of PFN1 in human cells, including a known dyskerin (DKC1)-installed Ψ site in TPI1 mRNA, which encodes triosephosphate isomerase. Moreover, we showed that PFN1 and DKC1 are crucial for regulating the stability and translation efficiency of TPI1 mRNA through modulating PFN1-Ψ interaction. Together, we identified PFN1 as a reader protein of Ψ in RNA and illustrated a potential role of PFN1-Ψ interaction in post-transcriptional regulation. These findings provide new insights into the functions of Ψ in RNA biology and in modulating the expression of an important metabolic enzyme.