ArticleBMC genomics2013
Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 51 citations in OpenAlex.
- mRNA Isoforms and Variants in Health and Disease.International journal of molecular sciences · 2025Review
- mRNA isoform switches during mouse zygotic genome activation.Cell proliferation · 2024Article
- miR-430 regulates zygotic mRNA during zebrafish embryogenesis.Genome biology · 2024Article
- Article
- Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish.Frontiers in cell and developmental biology · 2022Article
- Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation.The Journal of biological chemistry · 2021Article
- High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts.Genome biology · 2021Article
- Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish (G3 (Bethesda, Md.) · 2019Article
- Relative Abundance of Transcripts (F1000Research · 2019Article
- One-two punch mechanism of gene repression: a fresh perspective on gene regulation.Current genetics · 2018Review
- Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis.Cell · 2018Article
- Article
- Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos.BMC genomics · 2017Article
- Dose-dependent effects of gamma radiation on the early zebrafish development and gene expression.PloS one · 2017Article
- DNA signals at isoform promoters.Scientific reports · 2016Article
- Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing.PloS one · 2016Article
- Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs.PloS one · 2016Article
- EFTUD2 deficiency in vertebrates: Identification of a novel human mutation and generation of a zebrafish model.Birth defects research. Part A, Clinical and molecular teratology · 2015Article
- Identifying (non-)coding RNAs and small peptides: challenges and opportunities.BioEssays : news and reviews in molecular, cellular and developmental biology · 2015Review
- Potential Gene Interactions in the Cell Cycles of Gametes, Zygotes, Embryonic Stem Cells and the Development of Cancer.Frontiers in oncology · 2015Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.