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Transcriptome analyses of sex differential gene expression in brains of rare minnow (Gobiocypris rarus) and effects of tributyltin exposure.

ABSTRACT: RNA-sequencing was used to identify sex-biased gene expression in brains of rare minnow (Gobiocypris rarus) by comparing transcriptomic profiles between females and males. Furthermore, transcriptomic responses to 10?ng/L tributyltin (TBT) in both male and female brains were also investigated to understand whether TBT affects the identified sex-biased genes. Differentially expressed genes (DEGs) were identified using the IDEG6 web tool. In this article, we presented male- and female-biased DEGs, and up-regulated and down-regulated DEGs after TBT exposure. The raw reads data supporting the present analyses has been deposited in NCBI Sequence Read Archive (SRA, http://www.ncbi.nlm.nih.gov/Traces/sra) with accession number PRJNA376634. The data presented in this article are related to the research article entitled "Transcriptomic analyses of sexual dimorphism of rare minnow (G. rarus) brains and effects of tributyltin exposure" (doi: 10.1016/j.ecoenv.2018.02.049).

SUBMITTER: Zhang JL

PROVIDER: S-EPMC5996493 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Transcriptome analyses of sex differential gene expression in brains of rare minnow (<i>Gobiocypris rarus</i>) and effects of tributyltin exposure.

Zhang Ji-Liang JL Zhang Chun-Nuan CN Liu Min M Fan Ming-Zhen MZ Huang Mao-Xian MX

Data in brief 20180329

RNA-sequencing was used to identify sex-biased gene expression in brains of rare minnow (<i>Gobiocypris rarus</i>) by comparing transcriptomic profiles between females and males. Furthermore, transcriptomic responses to 10 ng/L tributyltin (TBT) in both male and female brains were also investigated to understand whether TBT affects the identified sex-biased genes. Differentially expressed genes (DEGs) were identified using the IDEG6 web tool. In this article, we presented male- and female-biased ...[more]

PMID: 29900293

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Project description:BackgroundMicroRNAs (miRNAs), which comprise a large family of endogenous small non-coding RNA molecules, play important roles in the regulation of gene expression in various biological processes. The Chinese rare minnow (Gobiocypris rarus) is a Chinese native fish species and is used extensively as an experimental fish in China; however, relevant biological data, especially miRNA transcriptome data, have not been well documented. To discover conserved and potential novel miRNAs in Chinese rare minnows, a pool of equal amounts of RNA obtained from 6 different adult rare minnow tissues (brain, eye, gill, liver, muscle and heart) was sequenced using illumina deep sequencing technology.ResultsIn the present study, 26,930,553 raw reads, representing 2,118,439 unique high-quality reads, were obtained from the pooled small RNA library. Using bioinformatics analysis, 352 conserved and 112 novel Chinese rare minnow miRNAs were first discovered and characterized in this study. Moreover, we found extensive sequence variations (isomiRs) in rare minnow miRNAs, including internal miRNA isomiRs and terminal isomiRs at both the 5' and 3' ends and nucleotide variants. Six conserved and 4 novel miRNAs were selected and validated in 6 different adult rare minnow tissues using quantitative real-time PCR (qPCR). The results showed that miR-30a, miR-30b, and Novel-37 are ubiquitously expressed in a variety of tissues. miR-16a, miR-9, miR-125b, miR-34a, and Novel-69 were predominantly expressed in the brain. Novel-115 and Novel-7 were highly expressed in gills, but were relatively weakly expressed in other tissues. These results provided the expression patterns of miRNA genes in Chinese rare minnow. Finally, based on bioinformatics predictions, we mainly found that Novel-94 and Novel-1b-5p were simultaneously targeted to the 3'UTR of Dmrt1, which controls sex determination and/or sexual differentiation in a variety of metazoans at different sites. Novel-29b targeted the 3'UTR of Foxl2, which is involved in the maintenance of ovarian function and the transcriptional regulation of gonadal differentiation-related genes. Novel-62 and Novel-53 targeted the 3'UTR of ERbeta1 and ERbeta2 (which regulate the transcription of target genes), respectively.ConclusionsRare minnow is a widely used model for assessing the risk of environmental pollution in China. Identifying and characterizing rare minnow miRNA genes is necessary to discover the biological function of miRNAs and to screen for new molecule biomarkers to assess the risk of environmental pollution in the future.

Project description:The fatty liver is one of the main problems in aquaculture. In addition to the nutritional factors, endocrine disrupter chemicals (EDCs) are one of the causes of fatty liver in fish. Bisphenol A (BPA) is a plasticizer widely used in the production of various plastic products and exhibits certain endocrine estrogen effects. Our previous study found that BPA could increase the accumulation of triglyceride (TG) in fish liver by disturbing the expression of lipid metabolism-related genes. How to recover the lipid metabolism disorder caused by BPA and other environmental estrogens remains to be explored. In the present study, Gobiocypris rarus was used as a research model, and 0.01% resveratrol, 0.05% bile acid, 0.01% allicin, 0.1% betaine, and 0.01% inositol were added to the feed of the G. rarus that exposed to 15 μg/L BPA. At the same time, a BPA exposure group without feed additives (BPA group) and a blank group with neither BPA exposure nor feed additives (Con group) were setted. The liver morphology, hepatosomatic index (HSI), hepatic lipid deposition, TG level, and expression of lipid metabolism-related genes were analyzed after 5 weeks of feeding. The HSI in bile acid and allicin groups was significantly lower than that in Con group. The TG in resveratrol, bile acid, allicin, and inositol groups returned to Con level. Principal component analysis of TG synthesis, decomposition, and transport related genes showed that dietary bile acid and inositol supplementation had the best effect on the recovery of BPA-induced lipid metabolism disorder, followed by allicin and resveratrol. In terms of lipid metabolism-related enzyme activity, bile acid and inositol were the most effective in recovering BPA-induced lipid metabolism disorders. The addition of these additives had a restorative effect on the antioxidant capacity of G. rarus livers, but bile acids and inositol were relatively the most effective. The results of the present study demonstrated that under the present dosage, bile acids and inositol had the best improvement effect on the fatty liver of G. rarus caused by BPA. The present study will provide important reference for solving the problem of fatty liver caused by environmental estrogen in aquaculture.

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Transcriptome analyses of sex differential gene expression in brains of rare minnow (Gobiocypris rarus) and effects of tributyltin exposure.

Publications

Transcriptome analyses of sex differential gene expression in brains of rare minnow (<i>Gobiocypris rarus</i>) and effects of tributyltin exposure.

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