Study on the Function of miRNA-155 Target Using Bioinformatics Methods

2013 ◽  
Vol 709 ◽  
pp. 858-861
Author(s):  
De Ming Han ◽  
Zi Jun Shen ◽  
Li Hui Zhao
Keyword(s):  
Protein Expression ◽  
Mirna Target ◽  
Target Gene ◽  
Target Genes ◽  
Gene Prediction ◽  
Diagnosis And Treatment ◽  
Transcriptional Level ◽  
Mirna Target Gene ◽  
Non Coding Rnas

MicroRNAs are small non-coding RNAs that act at the post-transcriptional level, regulating protein expression by repressing translation or destabilizing mRNA target. We searched information about miR-155 in miRBase. Target genes of miR-155 are predicted by four miRNA target gene prediction softwares. The result shows that miR-155 was involved in proliferation, differentiation and apoptosis. These results can contribute to further study on the role of microRNA in diagnosis and treatment of cancer.

scholarly journals MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity

2020 ◽  
Author(s):  
Ya-Lin Lu ◽  
Yangjian Liu ◽  
Matthew J. McCoy ◽  
Andrew S. Yoo
Keyword(s):  
Gene Expression ◽  
Mirna Target ◽  
Target Gene ◽  
Target Genes ◽  
Dependent Manner ◽  
Neuronal Function ◽  
Mirna Target Gene ◽  
Target Gene Expression ◽  
Human Neurons

SummaryNeuron-enriched microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124), direct cell fate switching of human fibroblasts to neurons when ectopically expressed by repressing anti-neurogenic genes. How these miRNAs function after the onset of the transcriptome switch to a neuronal fate remains unclear. Here, we identified direct targets of miRNAs by Argonaute (AGO) HITS-CLIP as reprogramming cells activate the neuronal program and reveal the role of miR-124 that directly promotes the expression of its target genes associated with neuronal development and function. The mode of miR-124 as a positive regulator is determined by a neuron-enriched RNA-binding protein, ELAVL3, that interacts with AGO and binds target transcripts, whereas the non-neuronal ELAVL1 counterpart fails to elevate the miRNA-target gene expression. Although existing literature indicate that miRNA-ELAVL1 interaction can result in either target gene upregulation or downregulation in a context-dependent manner, we specifically identified neuronal ELAVL3 as the driver for miRNA target gene upregulation in neurons. In primary human neurons, repressing miR-124 and ELAVL3 led to the downregulation of genes involved in neuronal function and process outgrowth, and cellular phenotypes of reduced inward currents and neurite outgrowth. Results from our study support the role of miR-124 promoting neuronal function through positive regulation of its target genes.

scholarly journals Association of Extracellular Signal-Regulated Kinase Genes With Myopia: A Longitudinal Study of Chinese Children

2021 ◽  
Vol 12 ◽  
Author(s):  
Haishao Xiao ◽  
Shudan Lin ◽  
Dandan Jiang ◽  
Yaoyao Lin ◽  
Linjie Liu ◽  
...  
Keyword(s):  
Longitudinal Study ◽  
Gene Network ◽  
Mirna Target ◽  
Target Gene ◽  
Target Genes ◽  
Chinese Children ◽  
Indirect Interaction ◽  
Mirna Target Gene ◽  
Extracellular Signal Regulated Kinase ◽  
Extracellular Signal

Graphical AbstractThe genes in the miRNA-target gene network represent the intersection of the target genes and the genes from String that had direct or indirect interaction relationships with significant genes.

scholarly journals Hsa-circ-0064636 regulation of the target gene VDAC1/UBE4A by hsa-miR-326/hsa-miR-503-5 in osteosarcoma

2021 ◽  
Author(s):  
Guohua Yan ◽  
Hanji Huang ◽  
Kanglu Li ◽  
Mingjun Zheng ◽  
Jiagang Qin ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Target Gene ◽  
Target Genes ◽  
Gene Prediction ◽  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Circular Rnas ◽  
Qrt Pcr ◽  
Eukaryotic Organisms

Abstract Background: Circular RNAs (circRNAs) are a subclass of noncoding RNAs that play a critical role in the regulation of gene expression in eukaryotic organisms. Recent studies have revealed the critical role of circRNAs in cancer progression. Yet, little is not well understood of hsa-circ-0064636 in osteosarcoma (OS).Methods: The differential expression of hsa-circ-0064636 in OS cell lines was verified by quantitative real-time PCR (qRT-PCR). Differentially expressed mRNAs and miRNAs were screened in OS mRNA and miRNA expression datasets. miRNAs that interacted with hsa-circ-0064636 were predicted by RNAhybrid, TargetScan and miRanda. and were further detected using RNAhybrid, TargetScan and miRanda. miRWalk, miRMap, and miRNAMap were used to perform target gene prediction on the intersected miRNAs to construct a circ-miRNA-mRNA interactor network. The target genes were then subjected to survival analysis using PROGgeneV2, which resulted in a circ-miRNA-mRNA interaction subnetwork with prognostic impact.Results: The qRT-PCR experiments successfully verified that hsa-circ-0064636 was significantly overexpressed in the OS cell line. Hsa-mir-326(miR-326) and hsa-mir-503-5p(miR-503-5p) are target miRNAs of hsa-circ-0064636 in the target genes obtained from the miR-326 and miR-503-5p screens. UBE4A and VDAC1 had a significant effect on prognosis. UBE4A is a target gene for miR-326, while VDAC1 is a target gene for miR-503-5p .Conclusion: hsa-circ-0064636 may be involved in OS development through acting as a sponge to inhibit miR-326 and miR-503-5p , thus regulating the expression of VDAC1 and UBE4A.

scholarly journals Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize

2019 ◽  
Vol 20 (14) ◽  
pp. 3480 ◽  
Author(s):  
Ziwen Li ◽  
Xueli An ◽  
Taotao Zhu ◽  
Tingwei Yan ◽  
Suowei Wu ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Mirna Target ◽  
Target Gene ◽  
Target Genes ◽  
Anther Development ◽  
Small Rna Sequencing ◽  
Mirna Target Gene ◽  
Gene Pairs ◽  
Gene Regulatory

The “competing endogenous RNA (ceRNA) hypothesis” has recently been proposed for a new type of gene regulatory model in many organisms. Anther development is a crucial biological process in plant reproduction, and its gene regulatory network (GRN) has been gradually revealed during the past two decades. However, it is still unknown whether ceRNAs contribute to anther development and sexual reproduction in plants. We performed RNA and small RNA sequencing of anther tissues sampled at three developmental stages in two maize lines. A total of 28,233 stably transcribed loci, 61 known and 51 potentially novel microRNAs (miRNAs) were identified from the transcriptomes. Predicted ceRNAs and target genes were found to conserve in sequences of recognition sites where their corresponding miRNAs bound. We then reconstructed 79 ceRNA-miRNA-target gene regulatory networks consisting of 51 known miRNAs, 28 potentially novel miRNAs, 619 ceRNA-miRNA pairs, and 869 miRNA-target gene pairs. More than half of the regulation pairs showed significant negative correlations at transcriptional levels. Several well-studied miRNA-target gene pairs associated with plant flower development were located in some networks, including miR156-SPL, miR159-MYB, miR160-ARF, miR164-NAC, miR172-AP2, and miR319-TCP pairs. Six target genes in the networks were found to be orthologs of functionally confirmed genes participating in anther development in plants. Our results provide an insight that the ceRNA-miRNA-target gene regulatory networks likely contribute to anther development in maize. Further functional studies on a number of ceRNAs, miRNAs, and target genes will facilitate our deep understanding on mechanisms of anther development and sexual plants reproduction.

scholarly journals RFMirTarget: A Random Forest Classifier for Human miRNA Target Gene Prediction

2012 ◽  
pp. 97-108 ◽  
Author(s):  
Mariana R. Mendoza ◽  
Guilherme C. da Fonseca ◽  
Guilherme L. de Morais ◽  
Ronnie Alves ◽  
Ana L. C. Bazzan ◽  
...  
Keyword(s):  
Random Forest ◽  
Mirna Target ◽  
Target Gene ◽  
Gene Prediction ◽  
Random Forest Classifier ◽  
Mirna Target Gene

scholarly journals miR-184 Inhibits Tumor Invasion, Migration and Metastasis in Nasopharyngeal Carcinoma by Targeting Notch2

2018 ◽  
Vol 49 (4) ◽  
pp. 1564-1576 ◽  
Author(s):  
Hong-Ming Zhu ◽  
Xue-Song Jiang ◽  
Hui-Zi Li ◽  
Lu-Xi Qian ◽  
Ming-Yu Du ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Cell Invasion ◽  
Mirna Target ◽  
Target Gene ◽  
Gene Prediction ◽  
Luciferase Reporter Assay ◽  
Luciferase Reporter ◽  
Reporter Assay ◽  
Mirna Target Gene ◽  
Dual Luciferase Reporter Assay

Background/Aims: A recent study found that dysregulated microRNA-184 (miR-184) is involved in the proliferation and survival of nasopharyngeal carcinoma (NPC). This study aimed to evaluate the detailed mechanisms of invasion, migration and metastasis of NPC cells. Methods: Quantitative reverse-transcription PCR (qRT-PCR) and Western blot were used to confirm the expression levels of miR-184 and Notch2. NPC cell invasion and migration were subsequently examined using in vitro cell invasion and wound-healing assays, respectively. MicroRNA (miRNA) target gene prediction databases and dual-luciferase reporter assay were adopted to validate the target genes of miR-184. Results: MiR-184 was downregulated in the NPC cell lines. The miR-184 inhibitor increased the number of invading NPC cells, whereas miR-184 mimics inhibited the invasive ability of such cells. The protein level of E-cadherin decreased, whereas those of N-cadherin and vimentin increased in the anti-miR-184 group. This result showed that miR-184 inhibited NPC cell invasion and metastasis by regulating EMT progression. MiRNA target gene prediction databases indicated the potential of Notch2 as a direct target gene of miR-184. Such a notion was then validated by results of dual-luciferase reporter assay. Notably, shRNANotch2 restrained the EMT and partially abrogated the inhibitory effects of miR-184 on EMT progression in NPC cells. Conclusion: MiR-184 functions as a tumour-suppressive miRNA targeting Notch2 and inhibits the invasion, migration and metastasis of NPC.

scholarly journals CHOP-Dependent Stress-Inducible Expression of a Novel Form of Carbonic Anhydrase VI

1999 ◽  
Vol 19 (1) ◽  
pp. 495-504 ◽  
Author(s):  
John Sok ◽  
Xiao-Zhong Wang ◽  
Nikoleta Batchvarova ◽  
Masahiko Kuroda ◽  
Heather Harding ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Target Gene ◽  
Target Genes ◽  
Direct Evidence ◽  
Nuclear Protein ◽  
Intracellular Form ◽  
Carbonic Anhydrase Vi ◽  
Responsive Element

ABSTRACT CHOP (also called GADD153) is a stress-inducible nuclear protein that dimerizes with members of the C/EBP family of transcription factors and was initially identified as an inhibitor of C/EBP binding to classic C/EBP target genes. Subsequent experiments suggested a role for CHOP-C/EBP heterodimers in positively regulating gene expression; however, direct evidence that this is the case has so far not been uncovered. Here we describe the identification of a positively regulated direct CHOP-C/EBP target gene, that encoding murine carbonic anhydrase VI (CA-VI). The stress-inducible form of the gene is expressed from an internal promoter and encodes a novel intracellular form of what is normally a secreted protein. Stress-induced expression of CA-VI is both CHOP and C/EBPβ dependent in that it does not occur in cells deficient in either gene. A CHOP-responsive element was mapped to the inducibleCA-VI promoter, and in vitro footprinting revealed binding of CHOP-C/EBP heterodimers to that site. Rescue of CA-VIexpression in c/ebpβ−/− cells by exogenous C/EBPβ and a shorter, normally inhibitory isoform of the protein known as LIP suggests that the role of the C/EBP partner is limited to targeting the CHOP-containing heterodimer to the response element and points to a preeminent role for CHOP in CA-VI induction during stress.

scholarly journals Advances in the role of miRNAs in the occurrence and development of osteosarcoma

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 1003-1011
Author(s):  
Guanyu Zhang ◽  
Yiran Li ◽  
Jiasheng Xu ◽  
Zhenfang Xiong
Keyword(s):  
Target Gene ◽  
Early Stage ◽  
Research Direction ◽  
Research Progress ◽  
Skeletal System ◽  
Translation Process ◽  
Non Coding Rnas ◽  
New Research ◽  
Post Transcriptional Regulation

AbstractOsteosarcoma (OS) is the most common primary malignant tumor of the skeletal system in the clinic. It mainly occurs in adolescent patients and the pathogenesis of the disease is very complicated. The distant metastasis may occur in the early stage, and the prognosis is poor. MicroRNAs (miRNAs) are non-coding RNAs of about 18–25 nt in length that are involved in post-transcriptional regulation of genes. miRNAs can regulate target gene expression by promoting the degradation of target mRNAs or inhibiting the translation process, thereby the proliferation of OS cells can be inhibited and the apoptosis can be promoted; in this way, miRNAs can affect the metabolism of OS cells and can also participate in the occurrence, invasion, metastasis, and recurrence of OS. Some miRNAs have already been found to be closely related to the prognosis of patients with OS. Unlike other reviews, this review summarizes the miRNA molecules closely related to the development, diagnosis, prognosis, and treatment of OS in recent years. The expression and influence of miRNA molecule on OS were discussed in detail, and the related research progress was summarized to provide a new research direction for early diagnosis and treatment of OS.

scholarly journals Identification of genes, pathways and transcription factor-miRNA-target gene networks and experimental verification in venous thromboembolism

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yiming Su ◽  
Qiyi Li ◽  
Zhiyong Zheng ◽  
Xiaomin Wei ◽  
Peiyong Hou
Keyword(s):  
Transcription Factor ◽  
Venous Thromboembolism ◽  
Cellular Response ◽  
Gene Network ◽  
Mirna Target ◽  
Target Gene ◽  
Vascular Endothelial Cell ◽  
Differentially Expressed ◽  
Ppi Network ◽  
Mirna Target Gene

AbstractVenous thromboembolism (VTE) is a complex, multifactorial life-threatening disease that involves vascular endothelial cell (VEC) dysfunction. However, the exact pathogenesis and underlying mechanisms of VTE are not completely clear. The aim of this study was to identify the core genes and pathways in VECs that are involved in the development and progression of unprovoked VTE (uVTE). The microarray dataset GSE118259 was downloaded from the Gene Expression Omnibus database, and 341 up-regulated and 8 down-regulated genes were identified in the VTE patients relative to the healthy controls, including CREB1, HIF1α, CBL, ILK, ESM1 and the ribosomal protein family genes. The protein–protein interaction (PPI) network and the transcription factor (TF)-miRNA-target gene network were constructed with these differentially expressed genes (DEGs), and visualized using Cytoscape software 3.6.1. Eighty-nine miRNAs were predicted as the targeting miRNAs of the DEGs, and 197 TFs were predicted as regulators of these miRNAs. In addition, 237 node genes and 4 modules were identified in the PPI network. The significantly enriched pathways included metabolic, cell adhesion, cell proliferation and cellular response to growth factor stimulus pathways. CREB1 was a differentially expressed TF in the TF-miRNA-target gene network, which regulated six miRNA-target gene pairs. The up-regulation of ESM1, HIF1α and CREB1 was confirmed at the mRNA and protein level in the plasma of uVTE patients. Taken together, ESM1, HIF1α and the CREB1-miRNA-target genes axis play potential mechanistic roles in uVTE development.

scholarly journals Identification and Classification of Hubs in microRNA Target Gene Networks in Human Neural Stem/Progenitor Cells following Japanese Encephalitis Virus Infection

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Sriparna Mukherjee ◽  
Irshad Akbar ◽  
Reshma Bhagat ◽  
Bibhabasu Hazra ◽  
Arindam Bhattacharyya ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Gene Networks ◽  
Mirna Target ◽  
Target Gene ◽  
Target Genes ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Neural Stem Progenitor Cells

ABSTRACT RNA viruses are known to modulate host microRNA (miRNA) machinery for their own benefit. Japanese encephalitis virus (JEV), a neurotropic RNA virus, has been reported to manipulate several miRNAs in neurons or microglia. However, no report indicates a complete sketch of the miRNA profile of neural stem/progenitor cells (NSPCs), hence the focus of our current study. We used an miRNA array of 84 miRNAs in uninfected and JEV-infected human neuronal progenitor cells and primary neural precursor cells isolated from aborted fetuses. Severalfold downregulation of hsa-miR-9-5p, hsa-miR-22-3p, hsa-miR-124-3p, and hsa-miR-132-3p was found postinfection in both of the cell types compared to the uninfected cells. Subsequently, we screened for the target genes of these miRNAs and looked for the biological pathways that were significantly regulated by the genes. The target genes involved in two or more pathways were sorted out. Protein-protein interaction (PPI) networks of the miRNA target genes were formed based on their interaction patterns. A binary adjacency matrix for each gene network was prepared. Different modules or communities were identified in those networks by community detection algorithms. Mathematically, we identified the hub genes by analyzing their degree centrality and participation coefficient in the network. The hub genes were classified as either provincial (P < 0.4) or connector (P > 0.4) hubs. We validated the expression of hub genes in both cell line and primary cells through qRT-PCR after JEV infection and respective miR mimic transfection. Taken together, our findings highlight the importance of specific target gene networks of miRNAs affected by JEV infection in NSPCs. IMPORTANCE JEV damages the neural stem/progenitor cell population of the mammalian brain. However, JEV-induced alteration in the miRNA expression pattern of the cell population remains an open question, hence warranting our present study. In this study, we specifically address the downregulation of four miRNAs, and we prepared a protein-protein interaction network of miRNA target genes. We identified two types of hub genes in the PPI network, namely, connector hubs and provincial hubs. These two types of miRNA target hub genes critically influence the participation strength in the networks and thereby significantly impact up- and downregulation in several key biological pathways. Computational analysis of the PPI networks identifies key protein interactions and hubs in those modules, which opens up the possibility of precise identification and classification of host factors for viral infection in NSPCs.

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