Abstract
BackgroundZebrafish 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).ResultsWe 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.ConclusionsThe 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.
Highlights
Zebrafish embryos are transcriptionally silent until activation of the zygotic genome during the 10th cell cycle
We identify numerous novel isoforms related to shifts in transcription start site (TSS), alternative splicing (AS) events and transcription termination sites (TTS), when comparing transcripts of maternal and zygotic origin coming from the same gene
Using H3K4 and H3K36 trimethylation data acquired by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq), we find that H3K4me3 can form relatively broad domains which cannot distinguish between closely spaced alternative TSSs, unless TSSs are linked to alternative promoters at distant locations
Summary
Zebrafish embryos are transcriptionally silent until activation of the zygotic genome during the 10th cell cycle. During the first ten cell cycles after fertilization, the zebrafish embryo is transcriptionally silent and consists of undifferentiated and rapidly dividing blastomeres [1]. Following ZGA, blastomeres divide less frequently and more asynchronously, they start to differentiate and migrate to form the three germ layers of the Previous studies have shown essential roles of activation and degradation of maternal transcripts in regulating the MBT and ZGA [5,6,7]. We and others have shown that the establishment of posttranslationally modified histones on specific genomic sites and DNA methylation play a role in transcriptional regulation around the time of ZGA by patterning developmental gene expression [9,10,11,12]. Several early transcriptomes have recently been published [5,13,14], little is known on the isoform-specific dynamics governing developmental transitions around the MBT
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