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Open Access Highly Accessed Research article

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

Håvard Aanes1, Olga Østrup23, Ingrid S Andersen23, Lars F Moen1, Sinnakaruppan Mathavan4, Philippe Collas23 and Peter Alestrom1*

Author Affiliations

1 BasAM, Norwegian School of Veterinary Science, 0033 Dep, Oslo, Norway

2 Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway

3 Norwegian Center for Stem Cell Research, 0317Oslo, Norway

4 Stem Cell and Developmental Biology, Genome Institute of Singapore, 60, Biopolis Street, #02-01, Genome 138672, Singapore

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BMC Genomics 2013, 14:331  doi:10.1186/1471-2164-14-331

Published: 15 May 2013

Abstract

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.

Keywords:
Zebrafish; Mid-blastula Transition; Zygotic Genome Activation; Alternative Splicing; Transcriptional Start Site; 3’UTR