miRNA Digger

miRNA Digger identifies novel microRNA (miRNA) genes by genome-wide screening of Dicer-mediated cleavage signals using degradome sequencing data to map miRNA precursor processing across plant and animal genomes.

Key Features:

• Systematic Genome-Wide Screening: Conducts comprehensive analysis of genomic sequences to identify potential miRNA candidates by detecting cleavage signals indicative of miRNA processing events.
• Utilization of Degradome Sequencing Data: Integrates degradome sequencing (a high-throughput sequencing approach) to map cleavage sites associated with miRNA precursor processing.
• Validation and Sensitivity: Validated on four organs of Arabidopsis thaliana, recovering a majority of known mature miRNAs and corresponding miRNA* sequences to demonstrate sensitivity and reliability.
• Discovery of Novel miRNA-miRNA* Pairs: Identified 30 novel miRNA–miRNA* pairs not listed in the miRBase database.
• Target Prediction and Validation: Facilitates target prediction and validated eleven miRNA–target interactions involving six newly identified miRNAs using degradome sequencing data.

Scientific Applications:

• Gene Regulation Studies: Systematically identifies novel miRNAs and predicts their targets to support investigations of post-transcriptional gene silencing by microRNAs.
• Plant Biology: Applied to Arabidopsis thaliana to discover organ-specific and previously unregistered miRNAs across multiple organs.
• Cross-Kingdom Applicability: Employs methods applicable to both plant and animal systems for discovery of miRNA precursors and processing sites.

Methodology:

Performs genome-wide screening for cleavage signals using degradome (high-throughput) sequencing data to map Dicer-mediated cleavage sites of miRNA precursors and applies degradome-based target prediction and validation.