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Next Generation Sequencing Facilitates Quantitative Analysis of feeding and fasting coilia nasus liver Transcriptomes

ABSTRACT: Purpose: To gain a comprehensive understanding of differential gene expression in anadromous C. nasus during feeding and fasting conditions. Methods: we characterized transcriptomics of C. nasus livers between feeding and fasting using RNA-seq Results:A total of 23,159 mRNA moleculeswere selected to identify the mechanisms of feeding and fasting. Our results provide insight into the activation of protein synthesis and energy metabolism, identification of key genes involved in food intake regulation, motivation of the fatty acid biosynthesis, glycolysis, TCA cycle and oxidative phosphorylation and decrease of amino acids and linoleic acid metabolism in feeding conditions compared to fasting. Conclusions:This is the first study describing differential gene expression and metabolic changes accompanying feeding and fasting in this interesting but endangered group. Our findings will be useful for future research on feeding characteristics, energy utilization and survival strategies of C. nasus.

ORGANISM(S): Coilia nasus

PROVIDER: GSE142614 | GEO | 2020/05/01

REPOSITORIES: GEO

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Project description:Background: Exposure to dichlorvos (DDVP), an organophosphorus pesticide, is known to result in neurotoxicity as well as other metabolic perturbations. However, the molecular causes of DDVP toxicity are poorly understood, especially in cells other than neurons and muscle cells. To obtain a better understanding of the process of non-neuronal DDVP toxicity, we exposed zebrafish to different concentrations of DDVP, and investigated the resulting changes in liver histology and gene transcription. Results: Functional enrichment analysis of genes affected by DDVP exposure identified a number of processes involved in energy utilization and stress response in the liver. The abundance of transcripts for proteins involved in glucose metabolism was profoundly affected, suggesting that carbon flux might be diverted toward the pentose phosphate pathway to compensate for elevated demand for energy and reducing equivalents for detoxification. Strikingly, many transcripts for molecules involved in Î²-oxidation and fatty acid synthesis were down-regulated. We found increases in message levels for molecules involved in reactive oxygen species responses as well as ubiquitination, proteasomal degradation, and autophagy. To ensure that the effects of DDVP on energy metabolism were not simply a consequence of poor feeding because of neuromuscular impairment, we fasted fish for 29 or 50 h and analyzed liver gene expression in them. The patterns of gene expression for energy metabolism in fasted and DDVP-exposed fish were markedly different.â Conclusion: We observed coordinated changes in the expression of a large number of genes involved in energy metabolism and responses to oxidative stress. These results argue that an appreciable part of the effect of DDVP is on energy metabolism and is regulated at the message level. Although we observed some evidence of neuromuscular impairment in exposed fish that may have resulted in reduced feeding, the alterations in gene expression in exposed fish cannot readily be explained by nutrient deprivation. Dichlorvos induced changes in gene expression in zebrafish were measured after 24 h exposures. A total of 20 arrays were processed with 4 replicates for each exposure condition (low, mid, and high) and 4 replicates for each of 2 control sets. Also, fasting induced changes in gene expression in zebrafish were measured after 24 hours fasting and 50 hours fasting. A total of 12 arrays were processed with 4 replicates for each exposure condition (no fasting, 24h fasting, 50h fasting).

Project description:This study integrates global transcriptional profiling and the metabolic perturbation induced by fasting and re-feeding. Genetic control of growth and development should be revealed by systematic modeling of metabolic and regulatory pathways. Chicken oligo arrays were used for transcriptional profiling in two time-course experiments. Two critical developmental stages were chosen: immediately after hatchling (Wk1) and prior to marketing of broiler chickens (Wk6). Only male chickens were used to simplify the experimental design. A RNA reference design was employed for microarray hybridization using two reference RNA pools derived from all individuals sampled at either Wk1 or Wk6. Microarray data was acquired using GenePix Pro software. Loess normalization and a linear mixed model were applied in data processing using the R statistical package with LIMMA software [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3]. The results show hundreds of differentially expressed genes, which are regulated by age and the metabolic perturbation of fasting and re-feeding. Numerous common genes were found at both developmental stages (Wk1 and Wk6) that could be candidates for controlling growth and development of chickens. Differential expression revealed by either microarray or qRT-PCR analyses of selected genes was highly consistent. QRT-PCR verification of genes acutely depressed by fasting includes AGO1, ANGTPL3, ATPCL, FASN, FAT, ME1, PPARG, SCD1, SREBP1 and THRSPA. Genes up-regulated by fasting were ALDOB, IL-15, LDHB, LIPIN2, PANK1, PPARA and UPP2. These genes are functionally assigned to metabolic enzymes, transcription factors, acute phase proteins, immune factors and involved in various pathways (i.e., fatty acid and amino acid metabolism, glycolysis, growth factor signaling and immune defense). Keywords: Hepatic transcripts, oligo-array, chicken, metabolic perturbation, fasting and re-feeding

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Next Generation Sequencing Facilitates Quantitative Analysis of feeding and fasting coilia nasus liver Transcriptomes

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