Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)

Exosomal miR-193b-5p as a regulator of LPS-induced inflammation in dairy cow mammary epithelial cells

Exosomes are a type of extracellular vesicle that act as shuttles, transporting certain genetic information to other cells. MiRNA cargo within exosomes can regulate gene expression at the transcriptional level. The objective of this study was to investigate the exosomal miRNAs that regulate lipopolysaccharide (LPS)-induced inflammation in dairy cow mammary alveolar (Mac-T) cells. We found two exosome miRNAs upregulated and five exosomal miRNAs downregulated, respectively, in the LPS-stimulated Mac-T cells. MiR-193b-5p was upregulated 6.3-fold in the LPS-stimulated cell-derived exosome. Target prediction results showed that nuclear factor kappa B (NF-κB) inhibitor delta (NFKBID), transforming growth factor-beta 1 induced transcript 1 (TGFB1I1), interleukin 22 (IL-22), TNF receptor superfamily member 11b (TNFRSF11B), and Janus kinase 3 (JAK3) might be the main target genes of miR-193b-5p. After treatment of Mac-T cells with the miR-193b-5p mimic, the phosphorylation levels of inhibitor of nuclear factor-kappa Bα (IκBα) and p65 were upregulated, the level of IL-6 mRNA was upregulated, and IL-1β, TNF-α, and TGF-β mRNA levels were downregulated. After treatment of Mac-T cells with miR-193b-5p inhibitor, the phosphorylation levels of IκBα and p65 were downregulated. In summary, these findings provide strong evidence that exosomal miR-193b-5p could be a regulator of LPS-induced inflammation in Mac-T cells and reveal a new role of exosomal miRNAs in regulating dairy cow mastitis.

Computational identification of microRNAs in the strawberry (Fragaria x ananassa) genome sequence and validation of their precise sequences by miR-RACE

In plants, microRNAs (miRNAs) play significant roles in post-transcriptional gene regulation and have been found to control many genes involved in different biological and metabolic processes. Extensive studies were carried out to discover miRNAs and analyze their functions in model plant species, such as in Arabidopsis and rice that have been reported. In this research, we used bioinformatics to predict microRNAs in an important strawberry rootstock cultivar to discover and validate precise sequences of microRNAs in strawberry. By adopting a range of filtering criteria, we obtained 59 potential miRNAs belonging to 40 miRNA families from the Fragaria vesca genome. Using two specific 5' and 3' miRNA RACE PCR reactions and a sequence-directed cloning method, we accurately determined 34 precise sequences of candidate miRNAs, while six other sequences exhibited some minor divergence in their termini nucleotides, and 19 miRNAs that could not be cloned owing to expression abundance may be too low or these mirRNAs predicted could not be existing in strawberry. Potential target genes were further predicted for the miRNAs above. The expression of the 16 miRNAs unreported and having exact sequences and their targets by experiment could be detected in different tissues of strawberry ranging from roots, stems, leaves, flowers and fruits by qRT-PCR and some of them showed differential expression in various tissues. The functional analysis of 16 miRNAs and their targets was carried out. Finally, we conclude that there are 34 mirRNAs in strawberry and their targets play vital roles not only in growth and development, but also in diverse physiological processes. These results show that regulatory miRNAs exist in agronomically important strawberry and might have an important function in strawberry growth and development.