Dynamic transcriptomic profiles of zebrafish gills in response to zinc depletion

Abstract

BackgroundZinc deficiency is detrimental to organisms, highlighting its role as an essential micronutrient contributing to numerous biological processes. To investigate the underlying molecular events invoked by zinc depletion we performed a temporal analysis of transcriptome changes observed within the zebrafish gill. This tissue represents a model system for studying ion absorption across polarised epithelial cells as it provides a major pathway for fish to acquire zinc directly from water whilst sharing a conserved zinc transporting system with mammals.ResultsZebrafish were treated with either zinc-depleted (water = 2.61 μg L-1; diet = 26 mg kg-1) or zinc-adequate (water = 16.3 μg L-1; diet = 233 mg kg-1) conditions for two weeks. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array. Of the genes represented the expression of a total of 333 transcripts showed differential regulation by zinc depletion (having a fold-change greater than 1.8 and an adjusted P-value less than 0.1, controlling for a 10% False Discovery Rate). Down-regulation was dominant at most time points and distinct sets of genes were regulated at different stages. Annotation enrichment analysis revealed that 'Developmental Process' was the most significantly overrepresented Biological Process GO term (P = 0.0006), involving 26% of all regulated genes. There was also significant bias for annotations relating to development, cell cycle, cell differentiation, gene regulation, butanoate metabolism, lysine degradation, protein tyrosin phosphatases, nucleobase, nucleoside and nucleotide metabolism, and cellular metabolic processes. Within these groupings genes associated with diabetes, bone/cartilage development, and ionocyte proliferation were especially notable. Network analysis of the temporal expression profile indicated that transcription factors foxl1, wt1, nr5a1, nr6a1, and especially, hnf4a may be key coordinators of the homeostatic response to zinc depletion.ConclusionsThe study revealed the complex regulatory pathways that allow the organism to subtly respond to the low-zinc condition. Many of the processes affected reflected a fundamental restructuring of the gill epithelium through reactivation of developmental programs leading to stem cell differentiation. The specific regulation of genes known to be involved in development of diabetes provides new molecular links between zinc deficiency and this disease. The present study demonstrates the importance of including the time-dimension in microarray studies.

Exploring Early Micronutrient Deficiencies in Rainbow Trout (Oncorhynchus mykiss) by Next-Generation Sequencing Technology – From Black Box to Functional Genomics

“…Kucukbay et al [45] showed that Zn supplementation decreased oxidative stress in rainbow trout. In zebrafish exposed to low (3 μg L −1 water and 26 mg kg −1 diet) or sufficient (16 μg L −1 water and 233 mg kg −1 diet) water and feed Zn concentrations, several general mechanisms in gill tissue were affected at deficiency, like down-regulation of developmental processes (26% of the genes in a 16K oligo nucleotide array), cell cycle, cell differentiation, gene regulation, butanoate metabolism, lysine degradation, protein tyrosin phosphatases, nucleobase, nucleoside and nucleotide metabolism, and cellular metabolic processes [46]. Genes among these groupings were associated to disorders like diabetes, bone tissue development and ionocyte proliferation.…”

“…Higher Zn absorption is found in low Zn diets [2]. Zheng et al [46] demonstrated the importance of including several time points for a better understanding of the homeostatic control mechanisms adjusting the fish body to changing Zn status.…”

Salinity- and population-dependent genome regulatory response during osmotic acclimation in the killifish (Fundulus heteroclitus) gill

“…HNF-4 is a transcription factor crucial for liver development, though it is expressed in some mammalian osmoregulatory tissues, such as kidney and intestine, for which its function remains to be determined (Grigo et al, 2008). The gene is also expressed in fish gill, where zinc deficiency induces transcription of HNF-4 and of genes enriched with HNF-4 binding elements (Zheng et al, 2010). Though a role in fish osmoregulation is novel, a homolog of HNF-4 appears crucial for coordinating osmoregulatory functions of excretory cells in nematode worms.…”

Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: transcriptomic and metabolic evidence

“…Xenopus gene identifiers were transformed into their human orthologs to improve the richness of the output [72, 73]. In order to differentiate functional enrichment due to up- and down- regulated genes, the DAVID tool was used on any gene found up- or down-regulated at at least one time point from the genes found to be differentially transcribed at any time point.…”