Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish

Area of Science:

• Developmental Biology
• Genomics
• Molecular Biology

Background:

• Zebrafish embryos exhibit transcriptional silence until zygotic genome activation (ZGA) at the 10th cell cycle.
• ZGA initiates cellular and morphological changes, including cell speciation and gastrulation.
• Previous studies focused on gene expression levels, necessitating isoform-specific analyses.

Purpose of the Study:

• To discover and quantify novel isoforms during zebrafish ZGA.
• To identify isoform switches occurring before and after ZGA.
• To provide a comprehensive view of transcriptomic changes at the isoform level.

Main Methods:

• Transcriptome sequencing of zebrafish embryos before and after ZGA.
• Isoform discovery and quantification using RNA sequencing data.
• Analysis of alternative splicing, transcriptional start sites, and 3' UTRs.

Main Results:

• Identification of novel isoforms and isoform switches in genes regulating cell adhesion, pluripotency, and DNA methylation.
• Detection of alternative splicing, altered transcriptional start sites, and 3' UTR changes.
• Over 1000 transcripts showed altered 3' terminal exon lengths post-ZGA; H3K36 trimethylation correlated with skipped exons.

Conclusions:

• Novel isoforms and switches identified regulate key transcriptional, cellular, and morphological events during ZGA.
• Isoform-related functional changes contribute significantly to early embryonic development.
• This dataset serves as a valuable resource for understanding early zebrafish transcriptomes.