MicroSalmon

MicroSalmon predicts microRNA response elements and cis-regulatory motifs within complete 3' untranslated regions (3'UTRs) assigned to full-length mRNA isoforms in the Atlantic salmon transcriptome to support analysis of miRNA regulation and post-transcriptional control.

Key Features:

• 3'UTRome compilation: Compiles complete 3'UTRs unambiguously assigned to specific full-length mRNA isoforms to create a species-specific 3'UTRome.
• miRNA target prediction: Uses RNAHybrid to predict miRNA response elements (MREs) across full-length transcripts, with a median of 1,487 target transcripts per miRNA and a median of 27 miRNAs per full-length transcript.
• Cis-regulatory motif identification: Employs UTRscan and the Teiresias algorithm to identify known vertebrate cis-regulatory motifs and putative novel motifs within 3'UTRs.
• Motif enrichment analysis: Detects over-represented low-complexity motifs enriched at 3'UTR termini and purine- or pyrimidine-rich motifs concentrated immediately downstream of the stop codon.
• Novel motif discovery: Identifies several novel complex motifs that are over-represented and potentially conserved among transcripts.
• Searchable repository: Provides a searchable repository to retrieve all full-length transcripts targeted by a specific miRNA or all miRNAs targeting a particular full-length transcript.

Scientific Applications:

• Post-transcriptional regulation mapping: Maps miRNA-target interactions and 3'UTR cis-elements to support study of mRNA stability and translation regulation in Atlantic salmon.
• Developmental biology: Investigates regulatory networks underlying developmental processes via miRNA and 3'UTR motif analyses.
• Stress response analysis: Analyzes miRNA and 3'UTR-mediated regulatory changes associated with stress responses.
• Disease mechanism exploration: Examines potential roles of miRNA targets and 3'UTR motifs in disease-related regulatory changes.

Methodology:

Integrates computational predictions with a curated set of Atlantic salmon full-length transcripts using RNAHybrid for miRNA target prediction and UTRscan plus the Teiresias algorithm for cis-regulatory motif identification.