PRMdb

PRMdb catalogs predicted tRNA and mRNA RNA modification sites across diverse plant species using analyses of RNA-seq, small RNA-seq, and degradome-seq to support epitranscriptomic studies.

Key Features:

• Extensive Data Analysis: Built from analysis of thousands of RNA-seq, small RNA-seq, and degradome-seq datasets to identify RNA modification candidates using HAMR (High-throughput Analysis of Modified Ribonucleotides).
• Data Sources: Raw sequencing data were sourced from NCBI SRA/GEO, Plant MPSS db, and the sRNA db at Danforth Center, with plant genomes and annotations from JGI phytozyme or Ensembl Plants.
• High-Confidence Modifications: Curates high-confidence tRNA and mRNA RNA modification sites, including novel sites, with candidates indicated for experimental validation by genomic PCR and reverse transcription PCR.
• Broad Applicability: Extends genome-wide RNA modification identification beyond Arabidopsis thaliana to a wide range of non-model plant species for comparative and functional analyses.

Scientific Applications:

• Functional Studies: Enables investigation of the roles of specific RNA modifications in plant gene expression and biology.
• Comparative Epigenetics: Supports comparative analyses of epitranscriptomic patterns across diverse plant species to study evolutionary and ecological variation.
• Validation Experiments: Provides candidate sites for experimental confirmation using genomic PCR and reverse transcription PCR.

Methodology:

Analysis of thousands of RNA-seq, small RNA-seq, and degradome-seq datasets using HAMR; raw data sourced from NCBI SRA/GEO, Plant MPSS db, and sRNA db at Danforth Center; plant genomes and annotations obtained from JGI phytozyme or Ensembl Plants.