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 pseudouridine site (Ψ) identification and functional annotation. 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 in silico 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.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Song B,Tang Y,Wei Z,Liu G,Su J,Meng J,Chen Kdoi
10.3389/fgene.2020.00088subject
Has Abstractpub_date
2020-03-12 00:00:00pages
88issn
1664-8021journal_volume
11pub_type
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