PmiRKB

PmiRKB provides integrated analyses of plant microRNAs (miRNAs) in Arabidopsis thaliana and Oryza sativa by combining SNP data, massively parallel signature sequencing, and PARE data to characterize pre-miRNAs, pri-miRNA expression, miRNA-target interactions, and miRNA precursor processing.

Key Features:

• SNP Module: Provides single nucleotide polymorphism data across seven Arabidopsis accessions and 21 rice subspecies and examines SNPs located within precursor miRNAs (pre-miRNAs) and miRNA-target RNA duplexes.
• Pri-miR Module: Profiles tissue-specific expression and transcriptional contexts of primary (pri-) and precursor miRNAs using massively parallel signature sequencing data.
• MiR-Tar Module: Validates thousands of miRNA-target interactions using parallel analysis of RNA ends (PARE) data.
• Self-reg Module: Uses PARE data to investigate miRNA precursor processing and self-regulation, including regulation by miRNA complementary strands (miRNA*).

Scientific Applications:

• Genetic variation analysis: Assess effects of SNPs within pre-miRNAs and miRNA-target duplexes on miRNA function and interactions.
• Tissue-specific expression profiling: Characterize pri- and pre-miRNA expression patterns across tissues to study developmental regulation.
• miRNA-target interaction validation: Confirm miRNA-mediated cleavage events and validate predicted miRNA-target pairs using PARE data.
• Autoregulatory mechanism investigation: Explore miRNA precursor processing and self-regulation, including roles of miRNA* strands.

Methodology:

Aggregates SNP datasets from seven Arabidopsis accessions and 21 rice subspecies; examines SNPs within pre-miRNAs and miRNA-target RNA duplexes and their potential impacts on pre-miRNA secondary structure and miRNA-target interactions; analyzes pri- and pre-miRNA expression using massively parallel signature sequencing; validates miRNA-target pairs and analyzes precursor processing and self-regulation using PARE (parallel analysis of RNA ends) data.