Functional study of RNA alternative splicing in zebrafish adaptation to low temperature

Alternative splicing (AS) is crucial for gene expression regulation during cold adaptation, yet its role in fish remains unclear. This study revealed tissue-specific AS patterns in zebrafish, with the gill exhibiting the highest AS frequency, followed by the skin, ovary and brain. Cold exposure significantly altered splicing sites across tissues, with exon skipping (SE) being the predominant AS form. Alternative splicing genes (ASGs) displayed strong tissue specificity, and splicing variability correlated with temperature, suggesting AS acts as a temperature-sensitive regulatory mechanism. Splicing factors, such as srsf7a, notably undergo AS, demonstrating their responsiveness to temperature changes. Key genes exhibiting differential splicing, including setd7 and mapta, present temperature-dependent isoforms. Under conditions of cold stress, zebrafish setd7 experiences cold-induced AS, resulting in the exclusion of exon 2 and the production of a truncated protein with a disrupted SET domain. This splicing event enhances zebrafish activity at lower temperatures. Simultaneously, mapta produces a 5R tau isoform via exon 7 skipping, which may dynamically regulate the balance between microtubule stability and plasticity during cold adaptation. Our transcriptome-wide analysis elucidates the AS regulatory mechanisms underlying the zebrafish response to cold stress and identifies key AS-mediated genes involved in cold adaptation, thereby providing a theoretical foundation for the molecular breeding of cold-tolerant aquaculture species.