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Series GSE40629 Query DataSets for GSE40629
Status Public on Nov 01, 2012
Title Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish
Organism Danio rerio
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Zebrafish embryos are transcriptional 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). 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 zygotically relative to the maternal transcript counterparts. ChIP-seq data mapped onto skipped exon events reveals a correlation between histone H3K36trimethylation peaks and the skipped exons, suggesting epigenetic marks being part of alternative splicing regulation. The novel isoforms and isoform switches reported here include regulators of the 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.
 
Overall design Examination H3K36me3 in zebrafish whole embryos at the Post-MBT stage
 
Contributor(s) Collas P, Aanes H
Citation(s) 23676078
Submission date Sep 05, 2012
Last update date May 15, 2019
Contact name Håvard Aanes
E-mail(s) havard.aanes@nvh.no
Organization name Norwegian School of Veterinary Science
Department Biochemistry
Street address Ullevålsveien 72
City Oslo
State/province Oslo
ZIP/Postal code 0883
Country Norway
 
Platforms (1)
GPL15583 Illumina Genome Analyzer IIx (Danio rerio)
Samples (2)
GSM998358 H3K36me3
GSM998359 Input
Relations
BioProject PRJNA174427
SRA SRP015415

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40629_RAW.tar 283.0 Mb (http)(custom) TAR (of TDF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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