Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish

Area of Science:

• Developmental Biology
• Genomics
• Molecular Biology

Background:

• Alternative splicing plays a crucial role in embryonic development, but its regulation in zebrafish embryogenesis remains largely uncharacterized.
• Previous research has primarily focused on alternative splicing in mammalian models like mice and humans.

Purpose of the Study:

• To construct a comprehensive alternative splicing atlas across 18 developmental stages in zebrafish.
• To investigate the dynamics and regulation of alternative splicing during zebrafish embryogenesis.
• To explore the relationship between alternative splicing, splicing factors, and transcriptional regulation.

Main Methods:

• Construction of an alternative splicing atlas using 18 time-course stages of zebrafish development.
• Detection and analysis of differential alternative splicing events.
• Gene expression profiling of splicing factors.
• Cluster analysis based on alternative splicing inclusion levels.
• Biological function and isoform switch analysis.

Main Results:

• Alternative splicing events are dynamically abundant, especially during the maternal-to-zygotic transition.
• Splicing factors exhibit stage-specific expression patterns, peaking during maternal-to-zygotic transition.
• Cluster analysis using alternative splicing inclusion levels improved performance.
• Alternative splicing plays significant roles in embryogenesis, with identified isoform switches offering insights into isoform regulation.
• Alternative splicing activation is synchronized with zygotic genome activation and coupled with transcription.

Conclusions:

• Alternative splicing is tightly regulated and coupled with transcription during zebrafish embryogenesis.
• Temporal expression dynamics of splicing factors, including co-orthologs, are critical.
• Alternative splicing inclusion levels offer a novel parameter for cluster analysis in developmental studies.