PRMD: an integrated database for plant RNA modifications

Abstract

The scope and function of RNA modifications in model plant systems have been extensively studied, resulting in the identification of an increasing number of novel RNA modifications in recent years. Researchers have gradually revealed that RNA modifications, especially N6-methyladenosine (m6A), which is one of the most abundant and commonly studied RNA modifications in plants, have important roles in physiological and pathological processes. These modifications alter the structure of RNA, which affects its molecular complementarity and binding to specific proteins, thereby resulting in various of physiological effects. The increasing interest in plant RNA modifications has necessitated research into RNA modifications and associated datasets. However, there is a lack of a convenient and integrated database with comprehensive annotations and intuitive visualization of plant RNA modifications. Here, we developed the Plant RNA Modification Database (PRMD; http://bioinformatics.sc.cn/PRMD and http://rnainformatics.org.cn/PRMD) to facilitate RNA modification research. This database contains information regarding 20 plant species and provides an intuitive interface for displaying information. Moreover, PRMD offers multiple tools, including RMlevelDiff, RMplantVar, RNAmodNet and Blast (for functional analyses), and mRNAbrowse, RNAlollipop, JBrowse and Integrative Genomics Viewer (for displaying data). Furthermore, PRMD is freely available, making it useful for the rapid development and promotion of research on plant RNA modifications.

Graphical Abstract

Figure 1.

Overall workflow of PRMD. PRMD provides comprehensive information about RNA modifications. All of the data generated by PRMD were deposited in a MySQL database and displayed in several convenient modules on web pages. In addition to the m⁶A modification, PRMD also contains other types of known RNA modifications (m¹A, m⁵C, m⁷G, ac⁴C, 2′-O-Me and pseudouridine) and additional related datasets derived from published research articles and related plant resources. Furthermore, PRMD provides several convenient tools for visualizing and analyzing data.

Figure 2.

Main functions of the PRMD database. (A) Outputs of statistical analyses, including peak gene feature distribution, gene type distribution, coverage plots for different features, boundary coverage for transcription start/end sites, boundary coverage for translation start/end sites and boundary coverage for splice sites. (B) Outputs of annotation analyses, including RNA characteristics of genes with modifications, mRNA metagene plot, enriched motifs, enriched Gene Ontology terms among the modified genes and enriched functional pathways among the modified genes. (C) Visualization of JBrowse data. JBrowse displays tracks of RNA modifications and other related annotations with genomic coordinates. (D) Visualization of mRNAbrowse data. mRNAbrowse shows tracks of RNA modifications and other related annotations. (E) Visualization of RNAlollipop data. RNAlollipop was designed to produce lollipop views of RNA modifications. (F) Outputs of the gene co-methylation network analysis. Dots represent gene names, whereas lines represent protein–protein interactions. Because of the limited number of samples, only four species are currently available for gene co-methylation analyses.

Figure 3.

Comparative analysis of m⁶A modifications in Oryza sativa. (A, B) RMlevelDiff comparison of m⁶A levels between samples. (C) Pheatmap of m⁶A levels. (D) Boxplot of m⁶A levels. (E) RMplantVar outputs, including a pie chart and a table.

Figure 4.

Comprehensive analysis of IPA1 in PRMD. (A) Outputs of the ‘Search’ module in PRMD revealed that IPA1 produces two transcripts with differing RNA modifications (m⁶A and m⁵C). (B) mRNAbrowse displays the tracks of mRNA modification peaks derived from different methods and different sources. (C) Lollipop view of RNA modifications. (D) JBrowse shows the tracks of m⁶A RNA modifications and other related annotations. (E) Details regarding IPA1. (F) Various annotations, including peak gene feature and type distributions, coverage plots for different features and boundary coverage for transcription start/end sites. (G) RNA characteristics of genes with modifications, RNA metagene plots, enriched motifs, enriched pathways and gene annotation information are presented in a tabular form.

Figure 5.

Classification and analyses of the co-methylation m⁶A modules in Oryza sativa. (A) Classification of co-methylated m⁶A modules. (B) Heatmap presenting the m⁶A indices of all co-methylation modules across all rice samples. (C) Density distributions of m⁶A peaks in different combined modules across the 5′ UTR, CDS and 3′ UTR. (D) Density distributions of log-transformed lengths of the internal exons with m⁶A peaks in different combined co-methylation modules. (E–H) In Oryza sativa, the following modules were associated with several traits: M5 (chlorophyll content and enzyme activity), M29 (root fresh weight and enzyme activity), M38 (panicle length/panicle number) and M40 (total soluble sugar content, leaf color and starch grain size).

Figure 6.

Analysis of wild rice (Oryza rufipogon) and two cultivated rice subspecies (Oryza sativa ssp. indica and Oryza sativa ssp. japonica). (A) Number of orthologous genes and m⁶A-modified genes among O. rufipogon, O. sativa ssp. indica and O. sativa ssp. japonica. (B) m⁶A methylation ratios for the one-to-one orthologous gene pairs of DXW81 versus WSSM and DXW81 vs ZH11. (C) Ka/Ks values for the one-to-one orthologous gene pairs of DXW81 versus WSSM and DXW81 vs ZH11. (D) GO enrichment analysis of the one-to-one orthologous gene pairs of DXW81 versus WSSM and DXW81 versus ZH11.