Computational methods for the identification of microRNA targets

Dai, Yang; Zhou, Xiaofeng

doi:10.2147/oab.s6902

Cited by 20 publications

(14 citation statements)

References 71 publications

(78 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…miRNA targets were predicted using the algorithms miRanda, miRDB, RNA22, and Targetscan [45]. To identify the genes commonly predicted by four different algorithms, the results of predicted targets were intersected using miRWalk [46].…”

Section: Methodsmentioning

confidence: 99%

microRNA-9 Suppresses the Proliferation, Invasion and Metastasis of Gastric Cancer Cells through Targeting Cyclin D1 and Ets1

et al. 2013

View full text Add to dashboard Cite

Recent evidence shows that altered microRNA-9 (miR-9) expression is implicated in the progression of gastric cancer. However, the exact roles and underlying mechanisms of miR-9 in the proliferation, invasion and metastasis of gastric cancer still remain unknown. In this study, miR-9 was found to be down-regulated and inversely correlated with the expression of cyclin D1 and v-ets erythroblastosis virus E26 oncogene homolog 1 (Ets1) in gastric cancer tissues and cell lines. Bioinformatics analysis revealed the putative miR-9 binding sites in the 3′-untranslated regions (3′-UTR) of cyclin D1 and Ets1 mRNA. Ectopic expression or knockdown of miR-9 resulted in responsively altered expression of cyclin D1, Ets1 and their downstream targets phosphorylated retinoblastoma and matrix metalloproteinase 9 in cultured gastric cancer cell lines SGC-7901 and AGS. In the luciferase reporter system, miR-9 directly targeted the 3′-UTR of cyclin D1 and Ets1, and these effects were abolished by mutating the miR-9 binding sites. Over-expression of miR-9 suppressed the proliferation, invasion, and metastasis of SGC-7901 and AGS cells in vitro and in vivo. Restoration of miR-9-mediated down-regulation of cyclin D1 and Ets1 by transient transfection, rescued the cancer cells from decrease in proliferation, migration and invasion. Furthermore, anti-miR-9 inhibitor promoted the proliferation, migration and invasion of gastric cancer cells, while knocking down of cyclin D1 or Ets1 partially phenocopied the effects of miR-9 over-expression. These data indicate that miR-9 suppresses the expression of cyclin D1 and Ets1 via the binding sites in their 3′-UTR, thus inhibiting the proliferation, invasion and metastasis of gastric cancer.

show abstract

Section: Methodsmentioning

confidence: 99%

microRNA-9 Suppresses the Proliferation, Invasion and Metastasis of Gastric Cancer Cells through Targeting Cyclin D1 and Ets1

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Five databases of predicted target mRNAs were selected: miRanda, miRDB, miRWalk, RNA22 and TargetScan. Because no program is consistently superior to all others and in order to reduce the probability of introducing false positives and/or negatives as much as possible, we selected the potential targets that were identified by at least three databases [18] , [33] . Predicted targets of some alternative mature miRNAs were only included in miRanda and miRWalk.…”

Section: Methodsmentioning

confidence: 99%

Integrated miRNA and mRNA Expression Profiling in Inflamed Colon of Patients with Ulcerative Colitis

et al. 2014

View full text Add to dashboard Cite

BackgroundUlcerative colitis (UC) is associated with differential colonic expression of genes involved in immune response (e.g. IL8) and barrier integrity (e.g. cadherins). MicroRNAs (miRNAs) are regulators of gene expression and are involved in various immune-related diseases. In this study, we investigated (1) if miRNA expression in UC mucosa is altered and (2) if any of these changes correlate with mucosal mRNA expression. Integration of mRNA and miRNA expression profiling may allow the identification of functional links between dysregulated miRNAs and their target mRNA.MethodologyColonic mucosal biopsies were obtained from 17 UC (10 active and 7 inactive) patients and 10 normal controls. Total RNA was used to analyze miRNA and mRNA expression via Affymetrix miRNA 2.0 and Affymetrix Human Gene 1.0ST arrays, respectively. Both miRNA and gene expression profiles were integrated by correlation analysis to identify dysregulated miRNAs with their corresponding predicted target mRNA. Microarray data were validated with qRT-PCR. Regulation of IL8 and CDH11 expression by hsa-miR-200c-3p was determined by luciferase reporter assays.ResultsWhen comparing active UC patients vs. controls, 51 miRNAs and 1543 gene probe sets gave significantly different signals. In contrast, in inactive UC vs. controls, no significant miRNA expression differences were found while 155 gene probe sets had significantly different signals. We then identified potential target genes of the significantly dysregulated miRNAs and genes in active UC vs. controls and found a highly significant inverse correlation between hsa-miR-200c-3p and IL8, an inflammatory marker, and between hsa-miR-200c-3p and CDH11, a gene related to intestinal epithelial barrier function. We could demonstrate that hsa-miR-200c-3p directly regulates IL8 and CDH11 expression.ConclusionDifferential expression of immune- and barrier-related genes in inflamed UC mucosa may be influenced by altered expression of miRNAs. Integrated analysis of miRNA and mRNA expression profiles revealed hsa-miR-200c-3p for use of miRNA mimics as therapeutics.

show abstract

“…After excision, mature miRNAs or siRNAs are loaded onto other protein factors, including the Argonaute proteins, to assemble the RNA-induced silencing complex (RISC) [ 8 ]. RISC then leads miRNA/siRNA to pair with specific mRNA targets to execute the translational repression or silencing [ 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

Alterations in SiRNA and MiRNA Expression Profiles Detected by Deep Sequencing of Transgenic Rice with SiRNA-Mediated Viral Resistance

Guo

Wang

et al. 2015

PLoS ONE

View full text Add to dashboard Cite

RNA-mediated gene silencing has been demonstrated to serve as a defensive mechanism against viral pathogens by plants. It is known that specifically expressed endogenous siRNAs and miRNAs are involved in the self-defense process during viral infection. However, research has been rarely devoted to the endogenous siRNA and miRNA expression changes under viral infection if the resistance has already been genetically engineered in plants. Aiming to gain a deeper understanding of the RNA-mediated gene silencing defense process in plants, the expression profiles of siRNAs and miRNAs before and after viral infection in both wild type and transgenic anti-Rice stripe virus (RSV) rice plants were examined by small RNA high-throughput sequencing. Our research confirms that the newly generated siRNAs, which are derived from the engineered inverted repeat construct, is the major contributor of the viral resistance in rice. Further analysis suggests the accuracy of siRNA biogenesis might be affected when siRNAs machinery is excessively used in the transgenic plants. In addition, the expression levels of many known miRNAs are dramatically changed due to RSV infection on both wild type and transgenic rice plants, indicating potential function of those miRNAs involved in plant-virus interacting process.

show abstract

Computational methods for the identification of microRNA targets

Cited by 20 publications

References 71 publications

microRNA-9 Suppresses the Proliferation, Invasion and Metastasis of Gastric Cancer Cells through Targeting Cyclin D1 and Ets1

microRNA-9 Suppresses the Proliferation, Invasion and Metastasis of Gastric Cancer Cells through Targeting Cyclin D1 and Ets1

Integrated miRNA and mRNA Expression Profiling in Inflamed Colon of Patients with Ulcerative Colitis

Alterations in SiRNA and MiRNA Expression Profiles Detected by Deep Sequencing of Transgenic Rice with SiRNA-Mediated Viral Resistance

Contact Info

Product

Resources

About