RNAcontext

RNAcontext infers RNA-binding protein (RBP) sequence and structural binding preferences by motif-finding from in vitro and in vivo RNA affinity-selected datasets.

Key Features:

• Enhanced Accuracy: Identifies RBP-specific binding preferences with greater accuracy than existing methodologies.
• Comprehensive Analysis: Evaluates both sequence and structural motifs to model RBP binding specificity.
• Validation through Control Proteins: Validated on published in vitro and in vivo RNA affinity-selected data, recovering known preferences for HuR, PTB, and Vts1p.
• Predictive Capability: Predicts novel RNA structure preferences for proteins including SF2/ASF, RBM4, FUSIP1, and SLM2, with SF2/ASF predictions aligning with reported in vivo binding sites.

Scientific Applications:

• Large-scale RBP preference mapping: Determining relative binding preferences of RBPs across diverse RNA sequences and structures using large-scale affinity-selected datasets.
• Post-transcriptional regulation studies: Investigating RBP roles in mRNA splicing, export, stability, and translation via identified sequence and structural motifs.
• Motif discovery and prediction: Predicting and characterizing novel sequence and structure motifs for RBPs to guide experimental validation.

Methodology:

Applies motif-finding to large-scale in vitro and in vivo RNA affinity-selected datasets to jointly model sequence and structural preferences of RBPs.