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Pseudouridine Identification and Functional Annotation with PIANO.

Jiahui Yao1, Cuiyueyue Hao2, Kunqi Chen3

  • 1Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China.

Methods in Molecular Biology (Clifton, N.J.)
|February 1, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces PIANO, a website for identifying pseudouridine (Ψ) sites in human RNA. PIANO accurately predicts Ψ locations and annotates their regulatory roles, aiding RNA modification research.

Keywords:
Functional annotationGenome-derived featurePseudouridine sitesRNA modificationWeb-server

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Pseudouridine (Ψ) is a prevalent RNA modification crucial for biological processes.
  • Accurate identification of Ψ sites is essential for understanding RNA function and regulation.
  • Existing methods for Ψ site identification may lack comprehensive annotation of regulatory mechanisms.

Purpose of the Study:

  • To develop and introduce PIANO, a novel website for pseudouridine (Ψ) site identification and functional annotation in humans.
  • To provide a high-accuracy prediction tool for putative Ψ sites.
  • To create a comprehensive database of experimentally-derived Ψ modifications and their regulatory roles.

Main Methods:

  • Development of a computational tool (PIANO) for predicting pseudouridine (Ψ) sites using machine learning models.
  • Testing prediction accuracy using six independent datasets, evaluating performance with Area Under the Curve (AUC) metrics.
  • Annotation of predicted Ψ sites for posttranscriptional regulatory elements, including miRNA targets, RNA-binding protein (RBP) regions, and splicing sites.

Main Results:

  • PIANO achieved high prediction accuracy for human Ψ sites, with an average AUC of 0.955 (full transcript model) and 0.838 (mature mRNA model).
  • The website annotates functional roles of putative Ψ sites, including miRNA-target interactions, RBP-binding sites, and splicing associations.
  • A comprehensive database containing over 4300 human Ψ modifications, derived from experimental data, is provided.

Conclusions:

  • PIANO offers a highly accurate and valuable resource for pseudouridine (Ψ) site identification and functional annotation.
  • The tool and database facilitate deeper research into the biological significance of RNA modifications.
  • PIANO is freely accessible, promoting advancements in RNA biology and related fields.