BRIO

BRIO identifies and catalogs sequence and secondary-structure motifs in RNA that are recognized by RNA-binding proteins (RBPs) to support analysis of RNA–protein interactions and post-transcriptional regulation.

Key Features:

• Motif types: Contains 2,508 sequence motifs and 2,296 secondary structure motifs.
• Experimental sources: Motifs derived from PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation), eCLIP (enhanced CLIP), and HITS-CLIP (High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation) datasets.
• Species coverage: Motifs identified in Homo sapiens and Mus musculus.
• RBP and domain linking: Motifs are linked to binding activities of 186 RNA-binding proteins and 69 protein domains.
• Motif search: Supports detailed motif searches across multiple compiled datasets.

Scientific Applications:

• Post-transcriptional regulation: Analysis of motifs to investigate regulation of gene expression and RNA stability mediated by RBPs.
• RNA–protein interaction mapping: Associating sequence and structural motifs with specific RBPs and protein domains.
• Disease and regulatory pathway investigation: Exploring molecular underpinnings of biological functions and diseases through motif–RBP associations.

Methodology:

Performs motif searches across compiled motif collections derived from PAR-CLIP, eCLIP, and HITS-CLIP experimental datasets.