Patterns of alternative splicing in response to cold acclimation in fish

Area of Science:

• * Molecular biology
• * Ecology and evolutionary biology
• * Genomics and transcriptomics

Background:

• * Phenotypic plasticity enables organisms to adapt to environmental changes, often involving gene expression modulation.
• * Gene expression changes can be quantitative (altered transcript amounts) or qualitative (alternative transcripts, e.g., alternative splicing).
• * While quantitative changes are well-studied, the role of qualitative changes, particularly alternative splicing, in phenotypic plasticity remains less understood.

Purpose of the Study:

• * To investigate the extent of qualitative gene expression changes, specifically alternative splicing, in response to cold acclimation.
• * To compare cold acclimation-induced alternative splicing across three fish species: Atlantic killifish, threespine stickleback, and zebrafish.

Main Methods:

• * RNA sequencing (RNA-seq) was performed on skeletal muscle tissue from Atlantic killifish, threespine stickleback, and zebrafish.
• * Analysis focused on identifying differentially expressed genes and genes exhibiting alternative splicing events associated with cold acclimation.

Main Results:

• * Cold acclimation induced alternative splicing in a substantial number of genes across species (426–866 genes).
• * Fewer genes showed alternative splicing compared to differential expression, but qualitative changes were significant.
• * Many alternatively spliced genes were also differentially expressed, with enrichment for muscle contraction functions.
• * A conserved set of 29 genes exhibited cold-acclimation-mediated splicing changes in all three species.

Conclusions:

• * Alternative splicing plays a significant role in the fish skeletal muscle response to cold acclimation, indicating substantial qualitative gene expression changes.
• * The findings suggest a conserved set of genes whose splicing patterns respond qualitatively to prolonged cold exposure across fish species.
• * Qualitative changes in gene expression, via alternative splicing, are a crucial mechanism for phenotypic plasticity in response to environmental challenges.