Additional file 4: Table S3. of Loss of function of myosin chaperones triggers Hsf1-mediated transcriptional response in skeletal muscle cells

GO term enrichment analysis of genes up- or down-regulated in unc45b mutants compared with wild type at 72 hpf. Cluster groups (1 and 2) were obtained from the hierarchical clustering of the 1411 genes regulated at 72 hpf (Additional file 3). (XLSX 43 kb

Transgenerational DNA Methylation Changes in Daphnia magna Exposed to Chronic γ Irradiation

Our aim was to investigate epigenetic changes in Daphnia magna after a 25-day chronic external γ irradiation (generation F0 exposed to 6.5 μGy·h^–1 or 41.3 mGy·h^–1) and their potential inheritance by subsequent recovering generations, namely, F2 (exposed as germline cells in F1 embryos) and F3 (the first truly unexposed generation). Effects on survival, growth, and reproduction were observed and DNA was extracted for whole-genome bisulfite sequencing in all generations. Results showed effects on reproduction in F0 but no effect in the subsequent generations F1, F2, and F3. In contrast, we observed significant methylation changes at specific CpG positions in every generation independent of dose rate, with a majority of hypomethylation. Some of these changes were shared between dose rates and between generations. Associated gene functions included gene families and genes that were previously shown to play roles during exposure to ionizing radiation. Common methylation changes detected between generations F2 and F3 clearly showed that epigenetic modifications can be transmitted to unexposed generations, most likely through the germline, with potential implications for environmental risk

Gene Responses in the Central Nervous System of Zebrafish Embryos Exposed to the Neurotoxicant Methyl Mercury

Methyl mercury (MeHg) is a neurotoxicant with adverse effects on the development of the nervous system from fish to man. Despite a detailed understanding of the molecular mechanisms by which MeHg affects cellular homeostasis, it is still not clear how MeHg causes developmental neurotoxicity. We performed here a genome-wide transcriptional analysis of MeHg-exposed zebrafish embryos and combined this with a whole-mount in situ expression analysis of 88 MeHg-affected genes. The majority of the analyzed genes showed tissue- and region-restricted responses in various organs and tissues. The genes were linked to gene ontology terms like oxidative stress, transport and cell protection. Areas even within the central nervous system (CNS) are affected differently resulting in distinct cellular stress responses. Our study revealed an unexpected heterogeneity in gene responses to MeHg exposure in different tissues and neuronal subregions, even though the known molecular action of MeHg would predict a similar burden of exposed cells. The overall structure of the developing brain of MeHg-exposed embryos appeared normal, suggesting that the mechanism leading to differentiation of the CNS is not overtly affected by exposure to MeHg. We propose that MeHg disturbs the function of the CNS by disturbing the cellular homeostasis. As these cellular stress responses comprise genes that are also involved in normal neuronal activity and learning, MeHg may affect the developing CNS in a subtle manner that manifests itself in behavioral deficits

Gene Responses in the Central Nervous System of Zebrafish Embryos Exposed to the Neurotoxicant Methyl Mercury

Methyl mercury (MeHg) is a neurotoxicant with adverse effects on the development of the nervous system from fish to man. Despite a detailed understanding of the molecular mechanisms by which MeHg affects cellular homeostasis, it is still not clear how MeHg causes developmental neurotoxicity. We performed here a genome-wide transcriptional analysis of MeHg-exposed zebrafish embryos and combined this with a whole-mount in situ expression analysis of 88 MeHg-affected genes. The majority of the analyzed genes showed tissue- and region-restricted responses in various organs and tissues. The genes were linked to gene ontology terms like oxidative stress, transport and cell protection. Areas even within the central nervous system (CNS) are affected differently resulting in distinct cellular stress responses. Our study revealed an unexpected heterogeneity in gene responses to MeHg exposure in different tissues and neuronal subregions, even though the known molecular action of MeHg would predict a similar burden of exposed cells. The overall structure of the developing brain of MeHg-exposed embryos appeared normal, suggesting that the mechanism leading to differentiation of the CNS is not overtly affected by exposure to MeHg. We propose that MeHg disturbs the function of the CNS by disturbing the cellular homeostasis. As these cellular stress responses comprise genes that are also involved in normal neuronal activity and learning, MeHg may affect the developing CNS in a subtle manner that manifests itself in behavioral deficits

Differential expression analysis in two-cells stage embryos and 96 hpf larvae obtained from DU-exposed adult fish.

<p>(A) MA-plot at the two-cells stage. (B) MA-plot at 96 hpf. (C) Five-ways diagram of all genes regulated in adult brain, testis, ovaries and in the progeny of DU-exposed fish at two-cells stage and 96 hpf. (D) Examples of expression changes in the progeny of DU-exposed fish of genes involved in DNA repair (<i>rad51d</i>, <i>rad50</i>, <i>rad2</i>), splicing (<i>isy1</i>, <i>syf2</i>), chromatin remodelling (<i>hat1</i> and <i>hdac5</i>), lipid transport (<i>apoeb</i>, <i>cetp</i>), oxidative stress (<i>duox</i>) and cell adhesion (<i>pcdh1gc6</i>) (all adjusted <i>p</i>-values (FDR) < 0.01; error-bars represent the standard deviation to the mean).</p

Expression analysis of electron transport chain complex genes in testis and brain of DU exposed fish and in their progeny at two-cells stage and 96 hpf.

<p>(A) Heatmap of adjusted <i>p</i>-values of genes involved in mitochondrial oxydo-reduction process (<i>n</i> = 101). The colour code displays the log10(adjusted <i>p</i>-value) from the differential expression analysis. (B) MA-plot focusing on the differential expression of the electron transport chain complex genes in the 96 hpf larvae (fold change as DU/C). Most of the genes are up-regulated in DU exposed larva.</p

Histological analysis of 96 hpf larvae from DU-exposed adult fish compared to controls.

<p>(A-A’) Toluidine-blue staining of the larva at the level of the trunk. Vacuole-like structures (appearing as white dots) are abundant in DU-treated larvae compared to controls. (B-C) Mitochondrial morphology in skeletal muscles observed by transmission electronic microscopy of control larvae. The inner mitochondrial membranes are dense and well visible (black arrow head). (B’-C’) Alteration of mitochondrial morphology and absence or decreases density of inner mitochondrial membranes (*) in larvae from DU-exposed fish. (D-E) High-resolution transmission electronic microscopy of skeletal muscles in controls and (D’-E’) in the 96 hpf larvae obtained from DU-exposed fish. Disruption of myofibres (red asterisks) and swelling of Z-bands are visible in DU larvae. Z- and A-bands are indicated. Triads constituted of t-tubes and the two flanking cisterna of the sarcoplasmic reticulum are visible in the controls (black arrows) but are absent or deformed in larvae from DU-treated fish (red arrows).</p

Heatmap of GO terms enriched in DU-exposed adult’s tissues and their progeny.

<p>The <i>p</i>-values from Fisher’s exact-test are indicated, as well as the associated GO terms. The datasets of up- and down-regulated genes used for the pathways analysis are indicated on the top of the heatmap (relative to fold change as DU exposed/control). The set of genes down-regulated in both adult brain and testis is also indicated. Yellow: Fisher’s exact test <i>p</i>-values < 0.01; black: non-significant enrichment.</p

Induction of protein chaperones expression following myofibre damage in the 96 hpf larvae from DU-exposed adult zebrafish.

<p>(A) MA-plot focusing on the differential expression of the 169 genes involved in cellular stress (from the ache mutant, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177932#sec002" target="_blank">Material and methods</a>) and their regulation in 96 hpf larvae obtained from DU exposed. Significant adjusted <i>p</i>-values < 0.01 are indicated in red and yellow. (B) Log2 fold change of specific protein-chaperon in the skeletal muscles (all adjusted <i>p</i>-values (FDR) < 0.01; error-bars represent the standard deviation to the mean).</p

Differential gene expression analysis in the adult tissues following a 10 days chronic exposure to DU.

<p>(A-C) MA-plot for the differential analysis in the adult brain (A), testis (B) and ovaries (C). Expression for each gene is shown on the x-axis as the log10 of the mean normalized expression, and the log2 of the fold change on y-axis. Significant adjusted <i>p</i>-values (FDR) < = 0.01 are highlighted in yellow to red, and non-significant changes in grey. (D) Venn diagram of genes mis-regulated in the brain, testis and ovaries. All genes significantly regulated (up- or down- regulated) were used to compare the three tissues. (E) Fold change of genes involved in regeneration and cell adhesion in DU exposed brain and testis compared to controls (all adjusted <i>p</i>-values (FDR) < 0.01; error-bars represent the standard deviation to the mean).</p