PRMdb: A Repository of Predicted RNA Modifications in Plants

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 well-documented 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 plants. RPMdb is available via http://www.biosequencing.cn/PRMdb/.

N6-methyladenosine (m6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence

“…A database-supported approach can greatly aid the course of research. Mammalian RNA modifications are accessible in many databases (MethylTranscriptome DataBase, RMBase, m 6 A 2Target, MeTDiff), in contrast with plant RNA modifications, which can be found only in one database: PRMdb ( Ma et al., 2020 ). The gathered data are based on the analysis of thousands of RNA-seq, degradome-seq, and small RNA-seq data from a broad range of plant species with the use of the tool HAMR (high-throughput analysis of modified ribonucleotide).…”

Transfer RNA-derived non-coding RNAs (tncRNAs): Hidden regulation of plants' transcriptional regulatory circuits

“…The SAM output was sorted and converted to BAM by samtools [61] (v1.10). The modification sites were predicted by HAMR (v1.2) (python hamr.py IN.bam REF.fa models/euk_trna_mods.Rdata OUT ath 30 10 0.05 H4 0.01 0.05 0.05) [48] , [62] . Further, modification sites only on mature tRNA and leader/trailer regions were counted.…”

Current technical advancements in plant epitranscriptomic studies

“…cn/PRMdb/) has also been gathering and annotating RNA modifications using public data, while PED (https://ngdc. cncb.ac.cn/ped/) and REDIdb (http://srv00.recas.ba.infn.it/ redidb/index.html) have been focusing on RNA editing events uncovered in plant research (Li et al, 2019;Lo Giudice et al, 2018;Ma et al, 2020).…”

“…To date, over 300 RNA modifications have been included by MODOMICS (the database of RNA modifications and their pathways; https://iimcb.genesilico.pl/modomics/) (Boccaletto et al., 2022). Moreover, PRMdb (http://biosequencing.cn/PRMdb/) has also been gathering and annotating RNA modifications using public data, while PED (https://ngdc.cncb.ac.cn/ped/) and REDIdb (http://srv00.recas.ba.infn.it/redidb/index.html) have been focusing on RNA editing events uncovered in plant research (Li et al., 2019; Lo Giudice et al., 2018; Ma et al., 2020).…”