IntEREst: intron-exon retention estimator.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Intron retention analysis offers insights into pre-mRNA splicing efficiency and regulation.
• Aberrant intron retention is linked to post-transcriptional regulation and human diseases.

Purpose of the Study:

• To introduce IntEREst, an R package for analyzing intron retention and exon-exon junction levels from RNA-seq data.
• To enable the analysis of both annotated and non-annotated intron retention events.
• To facilitate intra-sample and inter-sample comparisons of intron retention.

Main Methods:

• IntEREst accepts binary sequence alignment/map (.bam) files for genome-wide intron retention estimation.
• It includes functions for comparing specific intron subsets (e.g., U12-type vs. U2-type) and visualizing retention levels.
• Statistical analyses are adapted from DESeq2, edgeR, and DEXSeq, supporting both single-core and multi-core processing.

Main Results:

• IntEREst was used to analyze U12- and U2-type intron retention in human and plant RNA-seq datasets with ZRSR2 mutations.
• U12-type introns showed higher retention than U2-type introns in control samples, with retention exacerbated by ZRSR2 mutations.
• IntEREst identified retained introns with significant overlap with other methods, highlighting the impact of biological replicates and sequencing depth.

Conclusions:

• IntEREst provides a robust tool for analyzing intron retention events in RNA-seq data.
• ZRSR2 mutations significantly impact U12-type intron retention, suggesting a role in spliceosome-related diseases.
• Increased sequencing depth and replicates enhance the discovery of retained introns, with diminishing returns beyond 35 million reads.