Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA345605 | ENA |
REPOSITORIES: ENA
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Project description:To get insights into domain organization and functioning of the Danio rerio major α/β-globin locus (Mα/βGL), we have characterized profiles of histone H3 panacetylation across this locus in erythrocytes of adult fish and 18 dpf larvas. To identify enriched domains in our ChipSeq data we used our original protocol and peak caller MACS2. Histone acetylation profiles of Mα/βGL for adult and embryo cells reveal a breaking point in upstream region of the first embryo-larval gene βe1.There are two sub-segments of acetylation: sub-segment to the left of βe1 harbors adult-specific globin genes and is acetylated only in adult cells. Embryo sub-segment contains embryo-larval globin genes and is located to the right of βe1 gene. Acetylation in this subsegment was detected only in 18 dpf larva. Acetylation profile in adult subs-egment possess largest acetylation domain which covers two pairs of adult-stage globins: αa1, and βa1. High acetylation level in this domain well correlates with high expression level observed for these 4 genes in adult erythrocyte. Pattern of H3 panacetylation in 18 dpf larval erythrocytes differs strikingly from that for adult cells. Embryo-larval segment is fragmented in small domains co-located with gene bodies with gaps in intergenic regions. Adult subsegment in adult cells contains strong acetylation domain that cover 4 globin genes along with a part of intergenic regions and few smaller domains. Alternative stage-specific acetylation of subdomains and different pattern of embryonic-larval and adult domain acetylation strongly support the hypothesis of deep structural and functional segregation of stage-specific subdomains within Mα/βGL locus in zebrafish.
2017-01-01 | GSE86548 | GEO
Project description:The goal of this study was to compare RNA Seq profiles of Asian longhorned beetle larval guts feeding on two different substrates to identify key genes involved in woody tissue degradation, nutrient scavenging, and detoxification of host plant defensive compounds.
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Project description:The phenylpyrazole fipronil is a widely used insecticide designed to inhibit γ -amino-butyric acid (GABA) receptors, the major inhibitory neurotransmitter in the central nervous system. Fipronil has been detected in some water systems in the ng/L range, and is reported to be neurotoxic. To address the risks associated with fipronil exposure, we measured morphological, physiological, and molecular responses in zebrafish (Danio rerio) embryos following a 48 hour exposure (20 ng/L – 2 mg/L). Survival was not different than controls following treatments below 200 µg fipronil/L but was ~20% higher with concentrations above 200 µg fipronil/L. Once the embryos hatched, they underwent a 7 day depuration phase. At 9 days post-fertilization (9 dpf), body length and notochord length were not different than controls for any dose. To assess sub-lethal effects, transcriptome profiling was conducted in 9 dpf larvae following 48 hour exposure + 7 dpf depuration to environmentally relevant concentrations of fipronil (200 ng fipronil/L), as well as two higher concentrations of the pesticide (200 µg fipronil/L and 2 mg fipronil/L). Transcriptome profiling revealed that all three concentrations affected pathways related to chromosome condensation and the metabolism of estrogens and androgens as well as genes related to methylation. In addition, 200 ng fipronil/L down-regulated genes related to the circadian clock, histone and DNA methylation, and histone acetylation, while the highest dose increased networks related to immune function (e.g. lectin-induced complement pathway and the alternative complement pathway). The two highest concentrations of fipronil increased the expression of transcriptional networks associated with mitochondrial respiratory chain dysfunction and mitochondrial protein transport. As such, we exposed 24 hpf embryos to fipronil for 24 hours and measured oxygen consumption rate to assess mitochondrial function. There were no differences in basal and maximal respiration in the embryos nor ATP production, and fipronil did not affect mitochondrial bioenergetics. This study suggests that fipronil at environmentally relevant concentrations does not adversely affect the survival or morphology of fish embryos, however sub-lethal endpoints should be examined to more fully characterize the long term effects of fipronil exposure in larval fish.
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