A high-resolution mRNA expression time course of embryonic development in zebrafish

White, Richard; Collins, John; Sealy, Ian; Wali, Neha; Dooley, Christopher M.; Digby, Zsofia; Stemple, Derek L.; Murphy, Daniel N.; Billis, Konstantinos; Hourlier, Thibaut; Füllgrabe, Anja; Davis, Matthew P; Enright, Anton J.; Busch-Nentwich, Elisabeth M

doi:10.7554/elife.30860

Cited by 307 publications

(425 citation statements)

References 100 publications

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“…The morphological and developmental processes of zebrafish embryos at different stages as described byKimmel et al (1995) and the period of exposure to high ambient temperatures used in this study are illustrated inFigure 1c. In this study, a distinct reduction in survival ability was observed after treatment at 24 hpf in the pharyngula period (Prim-5,White et al, 2017), compared to the survived eggs at the pre-treatment (5 hpf) stage in both experimental groups, with a significant (p < 0.0002) lower survival ability in temperature-treated group (73.30% ± 0.58% in control vs. 70.19% ± 0.57% in treated groups). This stage of devel-…”

mentioning

confidence: 58%

Phenotypic plasticity induced using high ambient temperature during embryogenesis in domesticated zebrafish, Danio rerio

Hosseini

Brenig

Tetens

et al. 2018

Reprod Domestic Animals

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Contents Ambient temperature during early stages of life has a substantial effect on physiological processes, eliciting phenotypic plasticity during zebrafish developmental stages. Zebrafish are known to possess a noteworthy ability to modify their phenotype in dependence of environmental factors. However, there is a poor understanding of the effects of temperature during embryogenesis, which influences the biological functions such as survival ability and masculinization in later developmental stages. Since the middle embryonic phase (pharyngula period) is genetically the most conserved stage in embryogenesis, it is very susceptible to embryonic lethality in developmental processes of vertebrates. Here, we tested the effect of transient perturbations (heat shock) during early development (5–24 hr post‐fertilization; hpf) at 35°C compared to control group at 28°C, on survival ability of zebrafish to study the embryonic and post‐embryonic mortality. We studied the variation of heat‐induced masculinization among and across the families in response to high temperature. Furthermore, morphometric traits of adult zebrafish at different developmental time points were measured in order to estimate the temperature × sex interaction effect. We found the highest embryonic mortality around the gastrula and segmentation periods in both experimental groups, with significantly lower survival ability in the temperature‐treated group (73.30% ± 0.58% vs. 70.19% ± 0.57%, respectively). A higher hatching success was observed in the control group (71.08% ± 0.61%) compared to the heat‐induced group (67.95% ± 0.60%). A distinct reduction in survival ability was also observed in both experimental groups during the first two weeks after hatching, followed by a reduced level of changes thereafter. We found sex ratio imbalances across all families, with 25.2% more males under temperature treatment. Our study on growth performance has shown a positive effect of increased temperature on growth plasticity, with a greater impact on female fish in response to high ambient temperature.

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mentioning

confidence: 58%

Phenotypic plasticity induced using high ambient temperature during embryogenesis in domesticated zebrafish, Danio rerio

Hosseini

Brenig

Tetens

et al. 2018

Reprod Domestic Animals

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“…Moreover, chromatin accessibility increases during the stages preceding transcription activation (Figure 3a). As a control, we selected promoters of genes that are not expressed until two days post fertilization [16]. At these promoters, chromatin accessibility is extremely low and does not change from 256-cell to 80% epiboly.…”

Section: Chromatin Accessibility At Regulatory Elements Precedes Tranmentioning

confidence: 99%

“…The accessibility of promoters and enhancers prior to gene activation, as well as the increase in accessibility prior to transcription activation, are easily visible at specific gene loci. For example, the promoter and putative enhancer of gata6, a gene that is activated at dome stage [16,35], are accessible at 256cell stage and their accessibility increases prior to transcription ( Figure 3c). A similar relationship between accessibility and transcription activation can be observed for the regulatory elements of olig4 (activated at shield stage), and the experimentally validated enhancers of neurog (activated at 80% epiboly stage), ta (activated at sphere stage), and otx2 (activated at 80% epiboly stage) [36][37][38] (Figure 3c, Figure S5).…”

Section: Chromatin Accessibility At Regulatory Elements Precedes Tranmentioning

confidence: 99%

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Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

Pálfy

Schulze

Valen

et al. 2019

Preprint

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In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its relationship to gene activity during this transition remains poorly understood. Here, we generated chromatin accessibility maps from genome activation until the onset of lineage specification. During this period, chromatin accessibility increases at regulatory elements. This increase is independent of RNA polymerase II-mediated transcription, with the exception of the hyper-transcribed miR-430 locus. Instead, accessibility often precedes the transcription of associated genes. Loss of the maternal transcription factors Pou5f3, Sox19b, and Nanog, which are known to be required for zebrafish genome activation, results in decreased accessibility at regulatory elements. Importantly, the accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription.Our results show that the maternally provided transcription factors Pou5f3, Sox19b, and Nanog open up chromatin and prime genes for activity during zygotic genome activation in zebrafish.

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“…However, it is not late replicating until the end of gastrulation or bud stage (10 hpf) (Siefert et al, 2017). Previous work in zebrafish has found ZnF proteins on chromosome 4 to undergo robust expression from the initiation of zygotic transcription until mid-gastrula stage (White et al, 2017). Since many chromosome 4 genes are downregulated across ethanol-treated individuals during gastrulation, ethanol may interfere with replication timing, blocking the early-to-late replication switch, or chromatin remodeling.…”

Section: Discussionmentioning

confidence: 99%

Gene-environment interactions characterized by single embryo transcriptomics

Sidik¹,

Dixon²,

Kirby³

et al. 2019

Preprint

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Fetal Alcohol Spectrum Disorders (FASD) describes the full range of defects that result from prenatal alcohol exposure. The clinical diagnosis of Fetal Alcohol Syndrome (FAS) is the most severe outcome, characterized by facial dysmorphism and neurological deficits. Gene-ethanol interactions underlie susceptibility to FASD but we lack a clear understanding of the genetic risk factors. Here, we leverage the genetic tractability of zebrafish to address this problem. We first show that vangl2, a member of the Wnt/planar cell polarity (Wnt/PCP) pathway that mediates convergent extension movements, strongly interacts with ethanol during late blastula and early gastrula stages. Embryos mutant or heterozygous for vangl2 are sensitized to ethanol-induced midfacial hypoplasia. However, we have no understanding of the potential mechanism of this sensitization. We performed single-embryo RNA-Seq during early embryonic stages, to assess individual variation to the transcriptional response to ethanol and determine the mechanism of the vangl2-ethanol interaction. Transcriptional changes due to ethanol are indicative of increased oxidative stress and ion transport as well as reduced DNA replication and cell division. To identify the pathway(s) that are disrupted by ethanol we used these global changes in gene expression to identify small molecules, often pathway inhibitors, that mimic the effects of ethanol via the Library of Integrated Network-based Cellular Signatures (LINCS L1000) dataset. This dataset predicted that the Sonic Hedgehog (Shh) pathway inhibitor, cyclopamine, would mimic the effects of ethanol, despite ethanol not altering the expression levels of direct targets of Shh signaling. Indeed, we found that ethanol and cyclopamine strongly interact to disrupt midfacial development. Collectively, these results suggest that the midfacial defects in ethanol-exposed vangl2 mutants are due to an indirect interaction between ethanol and the Shh pathway. Vangl2 functions as part of a signaling pathway that regulates coordinated cell movements during midfacial development. 3Consistent with an indirect model, a critical source of Shh signaling that separates the developing eye field into bilateral eyes, allowing the expansion of the midface, becomes mispositioned in ethanol-exposed vangl2 mutants.

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A high-resolution mRNA expression time course of embryonic development in zebrafish

Cited by 307 publications

References 100 publications

Phenotypic plasticity induced using high ambient temperature during embryogenesis in domesticated zebrafish, Danio rerio

Phenotypic plasticity induced using high ambient temperature during embryogenesis in domesticated zebrafish, Danio rerio

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

Gene-environment interactions characterized by single embryo transcriptomics

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