BACKGROUND: Zebrafish embryos are transcriptionally silent until activation of 
the zygotic genome during the 10th cell cycle. Onset of transcription is 
followed by cellular and morphological changes involving cell speciation and 
gastrulation. Previous genome-wide surveys of transcriptional changes only 
assessed gene expression levels; however, recent studies have shown the 
necessity to map isoform-specific transcriptional changes. Here, we perform 
isoform discovery and quantification on transcriptome sequences from before and 
after zebrafish zygotic genome activation (ZGA).
RESULTS: We identify novel isoforms and isoform switches during ZGA for genes 
related to cell adhesion, pluripotency and DNA methylation. Isoform switching 
events include alternative splicing and changes in transcriptional start sites 
and in 3' untranslated regions. New isoforms are identified even for 
well-characterized genes such as pou5f1, sall4 and dnmt1. Genes involved in 
cell-cell interactions such as f11r and magi1 display isoform switches with 
alterations of coding sequences. We also detect over 1000 transcripts that 
acquire a longer 3' terminal exon when transcribed by the zygote compared to 
their maternal transcript counterparts. ChIP-sequencing data mapped onto skipped 
exon events reveal a correlation between histone H3K36 trimethylation peaks and 
skipped exons, suggesting epigenetic marks being part of alternative splicing 
regulation.
CONCLUSIONS: The novel isoforms and isoform switches reported here include 
regulators of transcriptional, cellular and morphological changes taking place 
around ZGA. Our data display an array of isoform-related functional changes and 
represent a valuable resource complementary to existing early embryo 
transcriptomes.