Steering Against Wind: A New Network of NamiRNAs and Enhancers

Li, Ying; Zou, Qingping; Yu, Wenqiang

doi:10.1016/j.gpb.2017.05.001

Cited by 19 publications

(18 citation statements)

References 52 publications

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“…MicroRNAs are noncoding RNAs that are only 18–25 nucleotides in length. Mature miRNAs have the ability to form RNA-induced silencing complexes with arginine proteins, which bind to the specific seed region of mRNA 3 ′-UTR, the target gene of miRNA, through base pairing, and achieve their biological function of inhibiting mRNA translation or facilitating mRNA degradation [ 3 ]. miRNAs are involved in the occurrence and the development of various diseases such as cancer, age-related cataract, and rheumatoid arthritis by affecting cell proliferation, cell differentiation, cell cycle, cell migration, and apoptosis [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

miR-214-3p Protects and Restores the Myocardial Tissue of Rat Myocardial Infarction Model by Targeting PTEN

Cheng

Jin

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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Myocardial infarction (MI), which results in myocardial cell dysfunction and irreversible loss, is one of the most serious health threats today. This study was started with rats, by which the consequence of miRNA expression dysregulation to the occurrence and progression of cardiovascular diseases was explored. We first conducted miRNA sequencing on the myocardial tissues separately from myocardial infarction treatment and sham operation treatment to clarify those differently expressed miRNAs; then, our experiment of functional verification of those key miRNAs was initiated so as to dig out the molecular mechanism behind the miRNA’s regulation in myocardial infarction. And it turned out that there were 32 upregulated miRNAs and 16 downregulated miRNAs according to our comparison from the myocardial infarction model group to the sham operation group; of all those upregulated, alteration in miR-214-3p expression was the most conspicuous. Overexpression of miR-214-3p greatly alleviated myocardial infarct area and ameliorated myocardial tissue structure, even reducing myocardial fibrosis and the devastation in the tissues. On the molecular level, miR-214-3p overexpression brought down both the apoptosis rate and cleaved caspase 3 expression. Besides that, we verified that PTEN is the target gene of miR-214-3p through a dual-luciferase assay. A cotransfection of miR-214-3p and PTEN brought about an obvious elevation in the myocardial infarct area, tissue damage, and fibrosis, even in the aspect of cellular apoptosis than a mere transfection of miR-214-3p. All the results above verified miR-214-3p′s effects in protecting myocardial tissues and reducing the infarct area, and it was reasonable to assume that those functions of miR-214-3p came into effect by targeting PTEN, which was then justified by the inversion to miR-214-3p′s protection via PTEN overexpression.

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Section: Introductionmentioning

confidence: 99%

miR-214-3p Protects and Restores the Myocardial Tissue of Rat Myocardial Infarction Model by Targeting PTEN

Cheng

Jin

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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“…A cell fate transition (cell fate commitment) occurs during the dynamical process of the early embryonic differentiation [18] , [19] . Generally, the dynamical process of early embryonic development can be regarded as the evolution of a nonlinear dynamical system, while the cell fate transition is viewed as a drastic or qualitative state shift at a bifurcation point [8] .…”

Section: Methodsmentioning

confidence: 99%

scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-Cell Graph Entropy

Zhong

Han

Zhang

et al. 2021

Genomics, Proteomics &Amp; Bioinformatics

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During early embryonic development, cell fate commitment represents a critical transition or “tipping point” of embryonic differentiation, at which there is a drastic and qualitative shift of the cell populations. In this study, we presented a computational approach, scGET, to explore the gene–gene associations based on single-cell RNA sequencing (scRNA-seq) data for critical transition prediction. Specifically, by transforming the gene expression data to the local network entropy, the single-cell graph entropy (SGE) value quantitatively characterizes the stability and criticality of gene regulatory networks among cell populations and thus can be employed to detect the critical signal of cell fate or lineage commitment at the single-cell level. Being applied to five scRNA-seq datasets of embryonic differentiation, scGET accurately predicts all the impending cell fate transitions. After identifying the “dark genes” that are non-differentially expressed genes but sensitive to the SGE value, the underlying signaling mechanisms were revealed, suggesting that the synergy of dark genes and their downstream targets may play a key role in various cell development processes. The application in all five datasets demonstrates the effectiveness of scGET in analyzing scRNA-seq data from a network perspective and its potential to track the dynamics of cell differentiation. The source code of scGET is accessible at https://github.com/zhongjiayuna/scGET_Project.

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“…Specifically, microRNAs are typically 19–25 nucleotides in size, and recognize the 3’ untranslated region of mRNA to mediate the post-transcriptional silencing of target genes ( 8 ). Furthermore, rather than inhibiting gene expression in the cytoplasm, microRNAs can target enhancers to active gene expression in the nucleus ( 9 ). Based on these mechanisms, the ceRNA network, constructed by lncRNA–microRNA–mRNA axes, plays a significant role in tumor origination and development, providing novel insights for tumor therapeutic targets and diagnostic biomarkers ( 10 ).…”

Section: Introductionmentioning

confidence: 99%

MiR-320b and miR-320d as Biomarkers to Predict and Participate in the Formation of Platinum Resistance in Ovarian Cancer Patients

et al. 2022

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Patients with ovarian cancer who receive platinum-based chemotherapy typically develop platinum resistance, which leads to tumor recurrence and mortality. Therefore, finding the underlying mechanisms and biomarkers is critical. A total of 51 platinum-resistant and 70 platinum-sensitive ovarian cancer patients were enrolled in this study. We examined the GSE131978 dataset in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database for differentially expressed long non-coding RNAs and messenger RNAs (mRNAs) between platinum-resistant and platinum-sensitive patients and completed a microRNA chip analysis. After filtering by Pearson correlation analysis, the competitive endogenous RNA (ceRNA) networks were subsequently constructed. Then, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology enrichment analyses about mRNAs in ceRNA networks were accomplished. More crucially, we demonstrated the differentially expressed microRNAs using quantitative real-time PCR and fluorescence in situ hybridization. The feasibility of microRNAs as biomarkers to predict platinum resistance and tumor recurrence was assessed using the receiver operating characteristic curve and survival analysis. MiR-320b and miR-320d exhibited high area under the curve values of 0.757 and 0.702, respectively. In our study, ceRNA networks including miR-320b and miR-320d probably provided novel insights for platinum resistance in ovarian cancer patients.

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Steering Against Wind: A New Network of NamiRNAs and Enhancers

Cited by 19 publications

References 52 publications

miR-214-3p Protects and Restores the Myocardial Tissue of Rat Myocardial Infarction Model by Targeting PTEN

miR-214-3p Protects and Restores the Myocardial Tissue of Rat Myocardial Infarction Model by Targeting PTEN

scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-Cell Graph Entropy

MiR-320b and miR-320d as Biomarkers to Predict and Participate in the Formation of Platinum Resistance in Ovarian Cancer Patients

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