Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella)

Abstract

The spleen is an important immune organ in fish. MicroRNAs (miRNAs) have been shown to play an important role in the regulation of immune function. However, miRNA expression profiles and their interaction networks associated with the postnatal late development of spleen tissue are still poorly understood in fish. The grass carp (Ctenopharyngodon idella) is an important economic aquaculture species in China. Here, two small RNA libraries were constructed from the spleen tissue of healthy grass carp at one-year-old and three-year-old. A total of 324 known conserved miRNAs and 9 novel miRNAs were identified by using bioinformatic analysis. Family analysis showed that 23 families such as let-7, mir-1, mir-10, mir-124, mir-8, mir-7, mir-9, and mir-153 were highly conserved between vertebrates and invertebrates. In addition, 14 families such as mir-459, mir-430, mir-462, mir-7147, mir-2187, and mir-722 were present only in fish. Expression analysis showed that the expression patterns of miRNAs in the spleen of one-year-old and three-year-old grass carp were highly consistent, and the percentage of miRNAs with TPM > 100 was above 39%. Twenty significant differentially expressed (SDE) miRNAs were identified. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that these SDE miRNAs were primarily involved in erythrocyte differentiation, lymphoid organ development, immune response, lipid metabolic process, the B cell receptor signaling pathway, the T cell receptor signaling pathway, and the PPAR signaling pathway. In addition, the following miRNA-mRNA interaction networks were constructed: immune and hematopoietic, cell proliferation and differentiation, and lipid metabolism. This study determined the miRNA transcriptome as well as miRNA-mRNA interaction networks in normal spleen tissue during the late development stages of grass carp. The results expand the number of known miRNAs in grass carp and are a valuable resource for better understanding the molecular biology of the spleen development in grass carp.

The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch (Sander lucioperca)

“…There was, for example, an up to 165-fold higher expression of mir-10 family members in the head kidney (slu-mir-10b-5p, -10c-5p) compared to the other organs ( Table 2 ). The enrichment of this family in this central immune organ of bony fish has already been demonstrated in studies on codfish ( Gadidae ) [ 21 ], snakehead ( Channidae ) [ 91 ], and carps ( Cyprinidae ) [ 67 , 92 ]. The mir-10 family seems to play an important regulatory role in the inflammation and innate immune response of vertebrates and invertebrates through the post-transcriptional regulation of Toll-like receptor signaling and associated transcription factors [ 93 , 94 ].…”

“…Mir-144-5p shows similarly high abundance in Atlantic cod spleen [ 21 ] and is associated with erythropoiesis [ 66 ]. Together with miR-101-3p, it is associated with macrophage function [ 67 ]. miRNA-2188, which is teleost-specific, is associated with immune responses and monocyte to macrophage maturation in fish [ 10 , 27 ], while the other teleost-specific miRNA that was highly abundant in the fingerling spleen, miR-8159-5p, is associated with immune response in fish [ 26 , 68 ].…”

The Link between Diabetes, Pancreatic Tumors, and miRNAs—New Players for Diagnosis and Therapy?

“…MicroRNAs are non-coding, single-stranded small RNAs, with an average length of 19–25 nucleotides. They are involved in many biological processes, such as cell growth, proliferation, differentiation, and organogenesis, and their main mechanism of action is to regulate gene function either by the degradation of mRNA or through the inhibition of mRNA translation [ 51 ].…”