Abstract:A web tool for information retrieval and analysis of soybean miRFNs and the relevant target functional gene networks can be accessed at SoymiRNet: http://nclab.hit.edu.cn/SoymiRNet.
“…Although small in number, miRNAs were found to control a large set of pathophysiological processes by the fact that multiple miRNAs often work interactively to control individual genes [29]. However, a large number of researches have so far focused on the role of individual miRNAs in different cancers, instead of the interaction among miRNAs.…”
Previous studies have found that miR-375 and miR-205 were significantly dysregulated in laryngeal squamous cell carcinoma, which contributed to the invasion and migration of LSCC. However, the mechanisms of miR-375 and miR-205 regulating the invasion and migration of LSCC remain unknown. qRT-PCR was performed in 40 pairs of tissue samples to investigate the expression of miR-375 and miR-205 in LSCC and paracarcinoma tissues. To investigate whether or not miR-375 and miR-205 regulated the invasion and migration of LSCC synergistically via AKT-mediated epithelial-mesenchymal transition, miR-375 mimic and miR-205 inhibitor were transfected into SNU899 cells and miR-375 inhibitor and miR-205 mimic were transfected into SNU899 cells, respectively, with or without AKT inhibitor. Then the expressions of miR-375 and miR-205 were validated by qRT-PCR, cell migration and invasion were determined by wound healing assay and transwell invasive assay, and western blot analysis was performed to detect the expression of related proteins. Our results showed that miR-375 and miR-205 regulated the invasion and migration of LSCC via AKT-mediated EMT synergistically. In conclusion, our findings provided not only new information about the molecular mechanism of miRNAs regulating invasion and migration of LSCC, but also a theoretical principle for potential targeting therapy of laryngeal squamous carcinoma.
“…Although small in number, miRNAs were found to control a large set of pathophysiological processes by the fact that multiple miRNAs often work interactively to control individual genes [29]. However, a large number of researches have so far focused on the role of individual miRNAs in different cancers, instead of the interaction among miRNAs.…”
Previous studies have found that miR-375 and miR-205 were significantly dysregulated in laryngeal squamous cell carcinoma, which contributed to the invasion and migration of LSCC. However, the mechanisms of miR-375 and miR-205 regulating the invasion and migration of LSCC remain unknown. qRT-PCR was performed in 40 pairs of tissue samples to investigate the expression of miR-375 and miR-205 in LSCC and paracarcinoma tissues. To investigate whether or not miR-375 and miR-205 regulated the invasion and migration of LSCC synergistically via AKT-mediated epithelial-mesenchymal transition, miR-375 mimic and miR-205 inhibitor were transfected into SNU899 cells and miR-375 inhibitor and miR-205 mimic were transfected into SNU899 cells, respectively, with or without AKT inhibitor. Then the expressions of miR-375 and miR-205 were validated by qRT-PCR, cell migration and invasion were determined by wound healing assay and transwell invasive assay, and western blot analysis was performed to detect the expression of related proteins. Our results showed that miR-375 and miR-205 regulated the invasion and migration of LSCC via AKT-mediated EMT synergistically. In conclusion, our findings provided not only new information about the molecular mechanism of miRNAs regulating invasion and migration of LSCC, but also a theoretical principle for potential targeting therapy of laryngeal squamous carcinoma.
“…Regulation by miRNAs may not always be through single target regulation. miRNA–miRNA interactions, where the expression of one miRNA is regulated by another miRNA, has been reported (Guo et al, 2012; Xu et al, 2014). Trans-acting miRNAs ( ta-siRNAs ) from TAS genes direct the cleavage of partially complimentary mRNAs as a regulatory mechanism (Vaucheret, 2005; Mallory and Bouche, 2008; Montgomery et al, 2008).…”
Section: Micrornas (Mirnas): Origin and Mechanism Of Gene Regulationmentioning
Sugarcane, one of the most photosynthetically efficient crops, is an important source of sugar and feedstock for green energy and co-generation. The high level of polyploidy and genomic peculiarities in this crop point towards a complex mechanism of regulation for the economically important traits like sugar content, cane yield related traits, resistance to biotic and abiotic stresses etc. The regulatory pathways for these traits comprise of a number of genes, transcription factors and different categories of RNAs like small interference RNAs (siRNAs), and Micro RNAs (miRNAs). MicroRNAs (miRNAs) are found to play an important regulatory role in many crops. As in other crops, several miRNAs have been identified in sugarcane too and these are speculated to have a role in regulating the various metabolic processes. Role of miRNAs in relation to drought tolerance has been studied to a great extent in this crop. miRNAs have been predicted to be linked to expression of other traits like disease resistance, salinity tolerance, waterlogging and axillary bud growth in sugarcane. miRNAs can have a significant role in biomass production in sugarcane, as reported in several biofuel crops. Till now, miRNAs linked to sugar accumulation have not been identified in sugarcane, but studies suggest an important role for miRNAs in sugar metabolic pathway in crops like Sorghum and switch grass. It is presumed that in sugarcane too, sugar accumulation as well as the other important metabolic pathways might be regulated to some extent by the miRNAs. The review examines the progress made in understanding the miRNA regulation in sugarcane and the extent to which miRNA mediated regulation can be utilized in sugarcane improvement.
“…The procedure for SoyFN construction is shown in Figure 1. Briefly, SoyFN construction comprises three parts: (i) measuring gene functional similarity based on GOA, which was implemented as a species-free gene functional similarity analysis tool (GFSAT) (19), inferring the SoyFGN based on the cluster coefficient threshold selection (to be published), which was visualized by Cytoscape Web (Figure 1a); (ii) measuring soybean miRNA functional similarity based on consideration of both the accessibility between miRNA and its target genes and the interactive information between target genes in a whole gene functional network (SoyFGN) (18), inferring the SoymiRFN based on the cluster coefficient threshold selection (18), which was visualized by Cytoscape Web (Figure 1b); and (iii) incorporating many other publicly accessed databases and tools to support and enhance the analyses of the soybean genomic and microRNomic interactome (Figure 1c). Figure 1.Procedure for SoyFN construction.…”
Section: Database Construction and Data Descriptionmentioning
confidence: 99%
“…Here, we present SoyFN, a database of soybean functional gene networks (SoyFGNs) and miRNA functional networks (SoymiRFNs) partially based on our previously published work (18, 19). SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol (HTTP) call.…”
Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene–gene, gene–microRNA (miRNA) and miRNA–miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3′-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics.Database URL:
http://nclab.hit.edu.cn/SoyFN
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