Histone H4 acetylation regulates behavioral inter-individual variability in zebrafish

Román, Ángel‐Carlos; Vicente-Page, Julián; Pérez‐Escudero, Alfonso; Carvajal-González, José María; Fernández-Salguero, Pedro M.; Polavieja, Gonzalo G. de

doi:10.1101/100230

Cited by 6 publications

(5 citation statements)

References 39 publications

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“…Plants are a promising system to examine the global properties of noise in gene expression, as phenotypic variability, also referred to as phenotypic instability, has been observed in multiple areas of plant growth and development. Inter‐individual phenotypic variability has also been observed in isogenic populations of other organisms (Zhang et al , ; Roman et al , ), but the model plant Arabidopsis thaliana presents the advantage of being an inbreeding species where heterozygosity is extremely low (Abbott & Gomes, ). Phenotypic variability in plants can occur both within and between individuals that are growing in the same conditions.…”

Section: Introductionmentioning

confidence: 99%

Widespread inter‐individual gene expression variability in Arabidopsis thaliana

Cortijo

Aydın

Ahnert

et al. 2019

Molecular Systems Biology

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A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered although it could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform, and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about inter‐individual transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24‐h time course. We identified hundreds of genes that exhibit high inter‐individual variability and found that many are involved in environmental responses, with different classes of genes variable between the day and night. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.

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Section: Introductionmentioning

confidence: 99%

Widespread inter‐individual gene expression variability in Arabidopsis thaliana

Cortijo

Aydın

Ahnert

et al. 2019

Molecular Systems Biology

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“…These motions rely on neuronal networks called central pattern generators, which generate periodic motor commands for rhythmic movements and involve reticulospinal neurons of the hindbrain, interneurons, and primary and secondary motorneurons (Dougherty and Kiehn 2010;Kullander 2005;Warp et al 2012). Between 3 to 9 dpf, the proportion of time the zebrafish spends in motion increases progressively, while inter-larval variations are also observed (Román et al 2018). Free-swimming larvae are regularly used in locomotor testing, where the larvae are randomly distributed in a well plate and their activity monitored by an automated video tracking system.…”

Section: Spontaneous Swimmingmentioning

confidence: 99%

Approaches to Test the Neurotoxicity of Environmental Contaminants in the Zebrafish Model: From Behavior to Molecular Mechanisms

Fitzgerald

Könemann

Krümpelmann

et al. 2021

Enviro Toxic and Chemistry

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The occurrence of neuroactive chemicals in the aquatic environment is on the rise and poses a potential threat to aquatic biota of currently unpredictable outcome. In particular, subtle changes caused by these chemicals to an organism's sensation or behavior are difficult to tackle with current test systems that focus on rodents or with in vitro test systems that omit whole-animal responses. In recent years, the zebrafish (Danio rerio) has become a popular model organism for toxicological studies and testing strategies, such as the standardized use of zebrafish early life stages in the Organisation for Economic Cooperation and Development's guideline 236. In terms of neurotoxicity, the zebrafish provides a powerful model to investigate changes to the nervous system from several different angles, offering the ability to tackle the mechanisms of action of chemicals in detail. The mechanistic understanding gained through the analysis of this model species provides a good basic knowledge of how neuroactive chemicals might interact with a teleost nervous system. Such information can help infer potential effects occurring to other species exposed to neuroactive chemicals in their aquatic environment and predicting potential risks of a chemical for the aquatic ecosystem. In the present article, we highlight approaches ranging from behavioral to structural, functional, and molecular analysis of the larval zebrafish nervous system, providing a holistic view of potential neurotoxic outcomes.

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“…Nevertheless, the presence of a catalytic domain and their protein architecture suggest that these proteins are active, potentially filling a gap of knowledge regarding histone acetylation in fishes (Best et al, 2018). Whereas most studies are primarily focused on zebrafish (He et al, 2014;Román et al, 2018), KAT and HDAC/Sirtuin mRNA expression was recently described in mangrove rivulus during gonad-embryogenesis (Fellous et al, 2019a), and in trout, where histones undergo acetylation during spermatogenesis (Best et al, 2018). In the context of climate-driven range shifts, for species considered to be climate migrants (including stickleback), the precise mechanistic basis of cold acclimation through sirtuin(s) expression (Teigen et al, 2015) should be elucidated, since histone deacetylase activity is known to mediate thermal plasticity in zebrafish (Seebacher and Simmonds, 2019).…”

Section: Histone Acetylationmentioning

confidence: 99%

Genome Survey of Chromatin-Modifying Enzymes in Threespine Stickleback: A Crucial Epigenetic Toolkit for Adaptation?

Fellous

Shama

2019

Front. Mar. Sci.

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Ocean environments are changing rapidly and marine organisms need to cope with these changes in order to survive, develop, and reproduce. To do so, organisms can either migrate, adapt in situ or acclimate via phenotypic plasticity. In this context, the emerging field of environmental epigenetics investigates the contribution of genetic and epigenetic information to adaptive potential of wild populations. Epigenetic modifications are based on the highly dynamic combination of DNA methylation, histone modifications, and non-coding RNAs, which may facilitate phenotypic plasticity through genotype-epigenotype-environment interactions, and can drive rapid evolution in wild populations. However, while knowledge of epigenetic contributions to phenotypes across different developmental and generational timescales is increasing for medical research model species, the mechanistic and synergistic action of these modifications remain comparatively understudied in ecological models such as teleost fishes. Here, we characterized the evolution of the gene toolkit involved in key molecular epigenetic pathways including DNA methylation, histone modifications, macroH2A histone, and miRNA biogenesis/turnover in threespine stickleback, a model species in evolution and ecology. We then investigated these genes within a phylogenetic context by comparing them in stickleback to human, mouse, chicken, tropical clawed frog, zebrafish, medaka, green spotted puffer, channel catfish, and mangrove rivulus. We found that, in general, conserved domains, in conjunction with their phylogenetic positions, suggest evolutionary conservation of putative enzyme activity in stickleback. However, molecular epigenetic pathways also revealed that teleost gene evolution is diversified and complex. Specifically, the number of genes, gene loss/duplication events, identified conserved domains, and putative protein lengths vary greatly from one species to another, particularly within fishes, which exhibit a potentially new class of histone deacetylases. This suggests different biological functions specific to fish species, and that the action of genes regulating epigenetic modifications in model species are not necessarily applicable to other related species. We integrate our results into recent advances concerning epigenetic mechanisms in teleosts, and conclude by discussing the necessity to delve deeper into the fundamental mechanics of epigenetic modifications in a wide array of taxa, particularly those relevant for assisted evolution, conservation, aquaculture, fisheries, and climate change-adaptation studies.

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Histone H4 acetylation regulates behavioral inter-individual variability in zebrafish

Cited by 6 publications

References 39 publications

Widespread inter‐individual gene expression variability in Arabidopsis thaliana

Widespread inter‐individual gene expression variability in Arabidopsis thaliana

Approaches to Test the Neurotoxicity of Environmental Contaminants in the Zebrafish Model: From Behavior to Molecular Mechanisms

Genome Survey of Chromatin-Modifying Enzymes in Threespine Stickleback: A Crucial Epigenetic Toolkit for Adaptation?

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