ArticleBMC genomics2017
Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 17 citations in OpenAlex.
- High-resolution mapping of embryonic genome activation unveils a decoupling of transcription activation from precocious H3K4me3 removal.Science advances · 2026Article
- Multi-omics reveals glycolipid metabolism processes during the early development of largemouth bass (Micropterus salmoides).BMC genomics · 2026Article
- Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish.bioRxiv : the preprint server for biology · 2025Article
- Dynamics in zebrafish development define transcriptomic specificity after angiogenesis inhibitor exposure.Archives of toxicology · 2025Article
- Dynamic Transcriptional Landscape of Grass Carp (International journal of molecular sciences · 2022Article
- Real age prediction from the transcriptome with RAPToR.Nature methods · 2022Article
- Transglutaminase Type 2 regulates the Wnt/β-catenin pathway in vertebrates.Cell death & disease · 2021Article
- Dynamic Expression and Gene Regulation of MicroRNAs During Bighead Carp (Frontiers in genetics · 2021Article
- Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs ofInternational journal of molecular sciences · 2020Article
- Expression Analysis of mRNA Decay of Maternal Genes duringInternational journal of molecular sciences · 2019Article
- Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis).BMC genomics · 2019Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage. On average one embryo per minute was analysed. The focus was on identification and description of the transcriptome dynamics of the expressed genes in this embryonic stage, rather than to biologically interpret profiles in cellular processes and pathways.
resultsIn the late blastula to mid-gastrula stage, we found 6,734 genes being expressed with low variability and rather gradual changes. Ten types of dynamic behaviour were defined, such as genes with continuously increasing or decreasing expression, and all expressed genes were grouped into these types. Also, the exact expression starting and stopping points of several hundred genes during this developmental period could be pinpointed. Although the resolution of the experiment was so high, that we were able to clearly identify four known oscillating genes, no genes were observed with a peaking expression. Additionally, several genes showed expression at two or three distinct levels that strongly related to the spawn an embryo originated from.
conclusionOur unique experimental set-up of whole-transcriptome analysis of 180 individual embryos, provided an unparalleled in-depth insight into the dynamics of early zebrafish embryogenesis. The existence of a tightly regulated embryonic transcriptome program, even between individuals from different spawns is shown. We have made the expression profile of all genes available for domain experts. The fact that we were able to separate the different spawns by their gene-expression variance over all expressed genes, underlines the importance of spawn specificity, as well as the unexpectedly tight gene-expression regulation in early zebrafish embryogenesis.
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