Integrated analysis of the responses of a circRNA-miRNA-mRNA ceRNA network to heat stress in rainbow trout (Oncorhynchus mykiss) liver

Abstract

Background With the intensification of global warming, rainbow trout (Oncorhynchus mykiss) suffer from varying degrees of thermal stimulation, leads to mass mortality, which severely restrict the development of aquaculture. Understanding the molecular regulatory mechanisms of rainbow trout under heat stress is useful to develop approaches to relieve symptoms. Results Changes in nonspecific immune parameters revealed that a strong stress response was caused in rainbow trout at 24 °C, so we performed multiple transcriptomic analyses of rainbow trout liver under heat stress (HS, 24 °C) and control conditions (CG, 18 °C). A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified. A ceRNA regulatory network was constructed and a total of 301 circRNA-miRNA and 51 miRNA-mRNA negative correlation pairs were screened, and three regulatory correlation pairs were predicted: novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some target genes involved in metabolic processes, biological regulation or response to stimulus were highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as protein processing in the ER, the estrogen signaling pathway, and the HIF-1 signaling pathway. Conclusions These results extend our understanding of the molecular mechanisms of the heat stress response and provide novel insight for the development of strategies that relieve heat stress.

Integrated Analysis of lncRNA and circRNA Mediated ceRNA Regulatory Networks in Skin Reveals Innate Immunity Differences Between Wild-Type and Yellow Mutant Rainbow Trout (Oncorhynchus mykiss)

“…For lncRNA, circRNA and mRNA quantification, the 20 μL reaction volume contained 10 μL of SYBR Premix Ex Taq II (2×), 1 μL of each the sense and antisense primer (10 μM), 0.5 μL of cDNA, 7.5 μL ddH 2 O. The mRNA, lncRNA and circRNA expression levels were normalized to β-actin ( 24 ). For miRNA quantification, the 20 μL reaction volume contained 10 μL of SYBR Premix Ex Taq II (2×), 0.4 μL of each sense and antisense primer (10 μM), 1.6 μL of cDNA, 7.6 μL of ddH 2 O.…”

“…CircRNAs are covalently closed circular molecule generated by head to-tail splicing at the splice sites ( 23 ). According to the theory of competing endogenous RNA (ceRNA), lncRNA and circRNA can act as ceRNAs through competitively binding common miRNA response elements (MREs), and forming complex miRNA-mediated ceRNA networks, resulting in suppression of miRNAs and the expression of corresponding target genes ( 24 ). In recent years, ceRNA has provided a new way to study immune mechanisms of fish, for instance, a study in miiuy croaker ( Miichthys miiuy ) reported that lncRNA NARL exhibits a positive regulatory role in inflammatory and antiviral responses via acting as a ceRNA for miR-217-5p to relieve its repressive effects on nucleotide-binding oligomerization domain containing 1 ( nod1 ) expression ( 25 ).…”

“…Under normal conditions fish maintain a healthy status by defending themselves against potential invaders using a repertoire of innate and specific defense mechanisms ( 27 ). However, prior researches mainly focused on identification and characterization of ceRNAs and ceRNA regulatory networks in fish spleen, liver, and intestine following artificial infection to explore the immune mechanisms of pathogen resistance ( 24 , 28 – 30 ), and no study on the involvement of ceRNA in fish skin without artificial infection has been documented. Owing to many biological and abiotic stresses presented in natural flowing water pond aquaculture environment, and intensified culture environment and high susceptibility to infectious disease make the industry vulnerable to disease outbreaks resulting in significant economic losses.…”

Function of Circular RNAs in Fish and Their Potential Application as Biomarkers

“…Due to the increase in ocean temperature, rainbow trout suffer from varying degrees of thermal stress, which leads to mass mortality and severely restricts their production. Quan et al [122] have reported novel_circ_003889-novelm0674-3p-hsp90ab1, novel_circ_002325-miR-18-y-HSPA13, and novel_circ_002446-novel-m0556-3p-hsp70 ceRNA networks involved in development of the molecular response to relieve heat stress. The significant differences in expression levels of HSP70 and HSP90 families under heat stress suggest that these protein families are involved in important regulatory pathways in the organismal response to heat stress.…”

miR‐434 and miR‐242 have a potential role in heat stress response in rainbow trout (Oncorhynchus mykiss)

“…Cells exposed to heat stress facilitate the recovery of the biological activities of denatured and abnormally condensed proteins via chaperones ( i.e ., heat shock proteins or HSPs), which confers adaptive protection within a certain duration. A few studies have indicated that miRNAs are closely related to heat stress; alternations in environmental temperature affect miRNA expression levels, consequently influencing target gene regulation, which further affect the state of heat stress in organism (Cqza et al ., 2019; Dalmay, 2013; Quan et al ., 2021). Although miRNA‐based studies are being widely conducted, the association between miRNAs and heat stress response remains to be comprehensively understood, particularly in aquatic organisms, such as rainbow trout.Rainbow trout is a cold‐water fish; they typically survive at 12–25°C and upon encountering elevated water temperatures they gradually weaken and may even die (Wang et al ., 2016; Xia et al ., 2017).…”