Song, Bowen, Tang, Yujiao, Wei, Zhen, Liu, Gang, Su, Jionglong, Meng, Jia 
ORCID: 0000-0003-3455-205X and Chen, Kunqi
(2020)
PIANO: A Web Server for Pseudouridine-Site (ψ) Identification and Functional Annotation.
FRONTIERS IN GENETICS, 11.
88-.
Abstract
Known as the "fifth RNA nucleotide", pseudouridine (Ψ or psi) is the first-discovered and most abundant RNA modification occurring at the Uridine site, and it plays a prominent role in a number of biological processes. Thousands of Ψ sites have been identified within different biological contexts thanks to the advancement in high-throughput sequencing technology; nevertheless, the transcriptome-wide distribution, biomolecular functions, regulatory mechanisms, and disease relevance of pseudouridylation are largely elusive. We report here a web server-PIANO-for <b>p</b>seudouridine site (Ψ) <b>i</b>dentification <b>a</b>nd fu<b>n</b>ctional ann<b>o</b>tation. PIANO was built upon a high-accuracy predictor that takes advantage of both conventional sequence features and 42 additional genomic features. When tested on six independent datasets generated from four independent Ψ-profiling technologies (Ψ-seq, RBS-seq, Pseudo-seq, and CeU-seq) as benchmarks, PIANO achieved an average AUC of 0.955 and 0.838 under the full transcript and mature mRNA models, respectively, marking a substantial improvement in accuracy compared to the existing <i>in silico</i> Ψ-site prediction methods, i.e., PPUS (0.713 and 0.707), iRNA-PseU (0.713 and 0.712), and PseUI (0.634 and 0.652). Besides, PIANO web server systematically annotates the predicted Ψ sites with post-transcriptional regulatory mechanisms (miRNA-targets, RBP-binding regions, and splicing sites) in its prediction report to help the users explore potential machinery of Ψ. Moreover, a concise query interface was also built for 4,303 known Ψ sites, which is currently the largest collection of experimentally validated human Ψ sites. The PIANO website is freely accessible at: http://piano.rnamd.com.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | pseudouridine sites, genome-derived feature, RNA modification, Web-server, functional annotation |
| Divisions: | Faculty of Science and Engineering > School of Electrical Engineering, Electronics and Computer Science |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 17 Aug 2021 07:35 |
| Last Modified: | 09 Oct 2023 17:59 |
| DOI: | 10.3389/fgene.2020.00088 |
| Open Access URL: | https://doi.org/10.3389/fgene.2020.00088 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3133789 |
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