Profiling miRNAs of Teleost Fish in Responses to Environmental Stress: A Review

Abstract

miRNAs are a class of endogenous and evolutionarily conserved noncoding short RNA molecules that post-transcriptionally regulate gene expression through sequence-specific interactions with mRNAs and are capable of controlling gene expression by binding to miRNA targets and interfering with the final protein output. The miRNAs of teleost were firstly reported in zebrafish development, but there are recent studies on the characteristics and functions of miRNAs in fish, especially when compared with mammals. Environmental factors including salinity, oxygen concentration, temperature, feed, pH, environmental chemicals and seawater metal elements may affect the transcriptional and posttranscriptional regulators of miRNAs, contributing to nearly all biological processes. The survival of aquatic fish is constantly challenged by the changes in these environmental factors. Environmental factors can influence miRNA expression, the functions of miRNAs and their target mRNAs. Progress of available information is reported on the environmental effects of the identified miRNAs, miRNA targets and the use of miRNAs in fish.

Keywords: environment factors; environment stress; fish; miRNA; target mRNA.

Figure 1

Regulation of NHE, NHERF1, NKA, NKCC, IGF-1 and AQP, etc., by miRNAs under salinity in fish. Second messengers induce the transcription of DNA. miRNAs regulate gene expression and function in target genes. They regulate transcription of the target genes and protein synthesis. NHE, mean Na⁺/H⁺-exchanger; NHERF, Na⁺/H⁺ exchanger regulatory factor 1; NKCC, mean Na⁺-K⁺-2Cl- cotransporter; NKA, mean Na⁺/K⁺-ATPase; AQP, mean Aquaporin; IGF, mean insulin growth factor.

Figure 2

Regulation of GATA1, MyoD, PER2, GHITM, HMOX1 and HSP90 etc. by miRNAs under temperature in fish. miRNAs can negatively regulate the transcription of DNA induced by second messengers. miRNAs regulate gene expression and function in target genes. They regulate transcription of the target genes and protein synthesis. GATA1, mean GATA binding protein 1; MyoD, Myoblast determination protein; PER2, mean period circadian regulator 2; GHITM, mean growth hormone inducible transmembrane protein; HMOX1, mean heme oxygenase 1; HSP90, mean heat shock protein 90.

Figure 3

Regulation of CASPASE3, VEGF, SOD, HIF-1a, PFKL, HK, LDH and DDX5, etc., by miRNAs under oxygen concentration in fish. Second messengers induce the transcription of DNA. miRNAs regulate gene expression and function in target genes. They regulate transcription of the target genes and protein synthesis. VEGF, mean vascular endothelial growth factor; SOD, superoxidase dismutase; HIF-1a, mean hypoxia-inducible factor 1a; HK, mean hexokinase; LDH, mean lactate dehydrogenase; DDX5, mean DEAD-Box Helicase 5.

Figure 4

Role of microRNAs in the regulation of insulin and liver metabolism including the upregulation of FAS, SREBF1, ACLY and downregulation of CPT1a, CPT1b. FAS, SREBF1, ACLY, CPT1a and CPT1b, etc., are regulated by miRNAs under feed in fish. FAS, mean Fatty acid synthase; SREBF1, sterol regulatory element binding transcription factor 1; ACLY, mean ATP citrate lyase; CPT1a, mean carnitine palmitoyl-transferase 1a; CPT1b, mean carnitine palmitoyl-transferase 1B.

Figure 5

Regulation of BCL2, CYB561D2, GPER, NRF2, P38MAPK, SDH and CYT-C, etc., by miRNAs under environmental chemicals and sea water metal elements in fish. Second messengers induce the transcription of DNA. miRNAs regulate gene expression and function in target genes. They regulate transcription of the target genes and protein synthesis. BCL2, mean B-cell lymphoma 2; CYB561D2, Cytochrome B561 Family Member D2; GPER, mean G protein-coupled estrogen receptor; NRF2, mean nuclear factor erythroid-2-related factor 2; P38MAPK, mean p38 mitogen-activated protein kinases; SDH, mean succinate dehydrogenase; CYT-C, mean cytochrome C; cAMP, cyclic adenosine monophosphate; cGMP, cyclic guanosine monophosphate.

Figure 6

Standard analysis process and prospect of environment-related miRNAs in fish. (A) Data sets download, (B) search of background knowledge, (C) read alignment, (D) identification and characterization of known and novel miRNAs, (E) target prediction, (F) downstream analysis.