PRMdb: A Repository of Predicted RNA Modifications in Plants
- 1 June 2020
- journal article
- research article
- Published by Oxford University Press (OUP) in Plant and Cell Physiology
- Vol. 61 (6), 1213-1222
- https://doi.org/10.1093/pcp/pcaa042
Abstract
Evidence is mounting that RNA modifications play essential roles in posttranscriptional regulation of gene expression. So far, over 150 RNA modifications catalyzed by distinct enzymes have been documented. In plants, genome-wide identification of RNA modifications is largely limited to the model species Arabidopsis thaliana, while lacking in diverse non-model plants. Here, we present PRMdb, a plant RNA modification database, based on the analysis of thousands of RNA-seq, degradome-seq and small RNA-seq data from a wide range of plant species using the welldocumented tool HAMR (high-throughput analysis of modified ribonucleotide). PRMdb provides a user-friendly interface that enables easy browsing and searching of the tRNA and mRNA modification data. We show that PRMdb collects high-confidence RNA modifications including novel RNA modification sites that can be validated by genomic PCR and reverse transcription PCR. In summary, PRMdb provides a valuable web resource for deciphering the epitranscriptomes in diverse plant species and will facilitate functional studies of RNA modifications in plant. RPMdb is available via http://www.biosequencing.cn/PRMdb/.Keywords
Funding Information
- National Science Foundation of China (31871321)
- Tianjin Rice Industrial Technology System of China (ITTRRS2018006)
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