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Coding/non-coding cross-talk in intestinal epithelium transcriptome gives insights on how fish respond to stocking density

Gonçalves, Ana Teresa, Núñez-Acuña, Gustavo, Détrée, Camille, Gallardo-Escárate, Cristian
Comparative biochemistry and physiology 2019 v.29 pp. 14-23
Oncorhynchus mykiss, aquaculture systems, biochemical pathways, cDNA libraries, complementary DNA, energy, gene expression regulation, homeostasis, intestinal mucosa, juveniles, messenger RNA, non-coding RNA, stocking rate, transcriptome, trout
Fish respond to increasing stocking density as a stressor, adjusting physiological functions to increase energy supply for coping with deleterious effects and adapting. These responses are complex and systemic, and the molecular mechanisms involved remain undetermined. One of the most sensitive organs to environmental and homeostatic disruptions is the intestine, and since it plays several vital functions, understanding the molecular underpinnings of this organ under deleterious conditions is imperative for health improvement in aquaculture systems. This study aimed to understand how different stocking densities of rainbow trout (Oncorhynchus mykiss) modulates the coding and non-coding RNAs profiling, that in turn, play key roles to maintain the fish homeostasis. For this, the intestine tissue of juvenile trout stocked for 30 days either at low (LD: 3 kg m−3) or high density (HD: 40 kg m−3) were sampled to isolate total RNA and then construct cDNA libraries for an illumina sequencing platform. Differential gene expression analysis revealed a generalized downregulation of transcripts, including coding and long non-coding RNAs (lncRNAs). Notably, significant differences in transcripts involved in metabolic pathways, as well as immune and epithelium integrity and stability related pathways were found. A high number of downregulated transcripts enriched these pathways, and a strong correlation was observed between the most differentially expressed transcripts and the highly expressed lncRNAs. This study suggests a cross-talk between coding and non-coding RNAs in the intestine of fish exposed to suboptimal conditions, providing new insights into the regulatory role of the lncRNAs on fish response to stressors.