iRNA-PseU: Identifying RNA pseudouridine sites
Open accessAbstract
As the most abundant RNA modification, pseudouridine plays important roles in many biological processes. Occurring at the uridine site and catalyzed by pseudouridine synthase, the modification has been observed in nearly all kinds of RNA, including transfer RNA, messenger RNA, small nuclear or nucleolar RNA, and ribosomal RNA. Accordingly, its importance to basic research and drug development is self-evident. Despite some experimental technologies have been developed to detect the pseudouridine sites, they are both time-consuming and expensive. Facing the explosive growth of RNA sequences in the postgenomic age, we are challenged to address the problem by computational approaches: For an uncharacterized RNA sequence, can we predict which of its uridine sites can be modified as pseudouridine and which ones cannot? Here a predictor called "iRNA-PseU" was proposed by incorporating the chemical properties of nucleotides and their occurrence frequency density distributions into the general form of pseudo nucleotide composition (PseKNC). It has been demonstrated via the rigorous jackknife test, independent dataset test, and practical genome-wide analysis that the proposed predictor remarkably outperforms its counterpart. For the convenience of most experimental scientists, the web-server for iRNA-PseU was established at http://lin.uestc.edu.cn/server/iRNA-PseU, by which users can easily get their desired results without the need to go through the mathematical details.
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- Authors
- Chen, W., Tang, H., Ye, J., Lin, H., & Chou, K.-C.
- Affiliations
- North China University of Science and Technology (CN)
- Southwest Medical University (CN)
- University of Electronic Science and Technology of China (CN)
- King Abdulaziz University (SA)
- Corresponding author
- Chen, Wei
- Lin, Hao
- Chou, Kuo-Chen
- Venue
- Molecular Therapy - Nucleic Acids
- Publisher
- Elsevier BV
- Published
- 2016
- Volume
- 5
- Pages
- e332
- ISSN
- 2162-2531 (ISSN-L)
- PMC
- PMC5330936
- OpenAlex
- W2598495276
- Cited by
- 291
- References
- 85
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 11 · 2023: 12 · 2022: 12 · 2021: 31 · 2020: 48 · 2019: 45 · 2018: 66 · 2017: 45 · 2016: 13
- FWCI
- 29.29
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular Therapy — Nucleic Acids (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- RNA modification, pseudouridine synthase, web server, RNA sequence analysis
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