Insplico

Insplico quantifies adjacent intron splicing order (AISO) across genomes using short and long RNA sequencing reads to analyze splicing order and its determinants.

Key Features:

• Compatibility with Sequencing Technologies: Processes short and long RNA sequencing reads to compute AISO metrics.
• Validation through Simulated Reads: Validated performance using simulated reads.
• Reproducibility of Known Patterns: Recapitulates previously reported AISO patterns and reveals biases associated with long read sequencing.
• Consistency Across Biological Contexts: Shows that AISO around individual exons is stable across cell and tissue types and under major spliceosomal disruptions, and conserved between human and mouse brains.
• Universal Feature Identification: Identifies a set of universal features associated with AISO across diverse animal and plant species.
• Focus on Tissue-Specific Exons: Analyzes tissue-specific exons including SRRM4 microexons and finds many microexons with non-canonical AISO where the downstream intron is spliced first.
• Potential Regulatory Mechanisms: Suggests two potential modes by which SRRM4 may regulate microexons in relation to AISO and other splicing features.

Scientific Applications:

• Gene expression and splicing regulation: Characterizing regulation of gene expression and alternative splicing through AISO patterns.
• Evolutionary and comparative genomics: Comparing AISO conservation and divergence across species, including human and mouse and broader animal and plant comparisons.
• Microexon and splicing factor studies: Investigating regulation of SRRM4-dependent microexons and their splicing order.

Methodology:

Analyzes short and long RNA-seq reads to quantify AISO and detect splicing-order patterns; validated using simulated reads; employs an algorithmic framework to identify biases and AISO-related patterns.