MREdictor

MREdictor predicts microRNA recognition elements (MREs) and miRNA target sites in mammalian mRNAs by integrating sequence complementarity and mRNA structural context to improve identification of miRNA-mRNA interactions.

Key Features:

• Incorporation of Pumilio Recognition Elements (PRE): Integrates the presence of PREs near predicted miRNA-binding sites to account for the influence of Pumilio proteins on miRNA accessibility.
• Two-Step Model for Duplex Pairing: Employs a two-step model for miRNA-MRE duplex pairing that aligns with structural data and accommodates imperfect seed matches.
• Focus on Poorly Accessible Regions: Identifies miRNA targets within regions of stable secondary structure, including less accessible sites in 3'-untranslated regions (UTRs).

Scientific Applications:

• miRNA target prediction in mammalian genes: Predicts MREs and miRNA binding sites to support studies of post-transcriptional gene regulation.
• Analysis of structured 3' UTR regions: Detects potential miRNA interactions within structurally complex or poorly accessible 3'-UTRs influenced by RNA secondary structure.
• Detection of non-canonical targeting: Identifies targets that involve imperfect seed matches beyond canonical seed-based prediction methods.

Methodology:

Integrates PRE presence near predicted sites, employs a two-step miRNA-MRE duplex pairing model that allows imperfect seed matches, and considers mRNA secondary-structure accessibility and sequence complementarity within 3'-UTRs.