Intron retention is dynamically regulated during zebrafish larval development and disrupted by high-fat diet

Intron retention (IR) is an understudied mode of alternative splicing with emerging roles in development and stress responses. Here, we present a comprehensive in vivo analysis of IR dynamics during zebrafish larval development and under environmental perturbation. Using deep poly(A)-selected RNA sequencing across three post-fertilization stages (4, 10, and 15 days), we identify IR as a dominant and developmentally regulated splicing event, affecting over 1,000 genes. Unexpectedly, differential IR occurs largely independently of transcript abundance, suggesting a distinct regulatory axis that modulates RNA output via isoform structure rather than expression level. Genes exhibiting IR are enriched in pathways critical to RNA metabolism, neurodevelopment, cell stress responses and genome maintenance—functions that are not captured by differential expression analysis alone. We further show that exposure to a high-fat diet (HFD) reshapes the IR landscape, eliciting both shared and diet-specific splicing responses. Strikingly, some introns display opposing retention dynamics under HFD compared to normal development, highlighting the context-dependent responsiveness of IR regulation. Together, our findings position IR as a selective and environmentally responsive mechanism that contributes to shaping the transcriptome during vertebrate development.