IMEter

IMEter predicts intron-mediated enhancement (IME) signals from genomic sequences to identify introns and sequence motifs that can increase gene expression across eukaryotes.

Key Features:

• Comparative Genomic Analysis: Performs comparative analyses of sequenced plant genomes to identify conserved IME signals, noting conservation in multicellular plants and lack of recognizable signals in algae.
• Signal Localization and Composition: Identifies IME signals preferentially located toward the 5'-end of first introns and enriched in 5'-UTRs and coding regions near transcription start sites, and distinguishes compositionally distinct promoter-proximal and distal introns.
• Predictive Capability: Predicts presence of IME signals using sequence-profile-based scoring that assesses how well individual introns match a promoter-proximal intron profile.
• Functional and Evolutionary Insights: Detects dispersed sequences and overrepresented candidate motifs in first introns and correlates motif presence with expression effects to enable cross-species comparisons such as between Arabidopsis thaliana and Oryza sativa.

Scientific Applications:

• Gene Expression Optimization: Identify or engineer introns that enhance expression of target genes for use in agricultural biotechnology to improve crop traits.
• Functional Genomics Studies: Investigate the regulatory roles of introns in gene expression across different tissues and developmental stages.
• Evolutionary Biology Research: Examine conserved IME signals across species to study conservation and divergence of gene regulatory mechanisms.

Methodology:

Performs genome-wide analyses of eukaryotic sequence data including comparative genomics, sequence-profile-based prediction of IME signals, and motif overrepresentation analysis of first introns.