scholarly journals miR-TV: an interactive microRNA Target Viewer for microRNA and target gene expression interrogation for human cancer studies

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Chao-Yu Pan ◽  
Wen-Chang Lin
Keyword(s):  
Gene Expression ◽  
Clinical Data ◽  
Mirna Expression ◽  
Mirna Target ◽  
Target Gene ◽  
Biological Data ◽  
Expression Levels ◽  
Target Gene Expression ◽  
Cellular Processes ◽  
Interactive Interface

Abstract MicroRNAs (miRNAs) have been identified in many organisms, and they are essential for gene expression regulation in many critical cellular processes. The expression levels of these genes and miRNAs are closely associated with the progression of diseases such as cancers. Furthermore, survival analysis is a significant indicator for evaluating the criticality of these cellular processes in cancer progression. We established a web tool, miRNA Target Viewer (miR-TV), which integrates 5p-arm and 3p-arm miRNA expression profiles, mRNA target gene expression levels in healthy and cancer populations, and clinical data of cancer patients and their survival information. The developed miR-TV obtained miRNA-seq, mRNA-seq and clinical data from the Cancer Genome Atlas and potential miRNA target gene predictions from miRDB, targetScan and miRanda. The data presentation was implemented using the D3 javascript toolkit. The D3 toolkit is frequently used to provide an easy-to-use interactive interface. Our miR-TV provides a user-friendly and interactive interface, which can be beneficial for biomedical researchers to freely interrogate miRNA expression information and their potential target genes. We believe that such a data visualization bioinformatics tool is excellent for obtaining information from massive biological data. Database URL: http://mirtv.ibms.sinica.edu.tw

scholarly journals Profiling the Abiotic Stress Responsive microRNA Landscape of Arabidopsis thaliana

Plants ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 58 ◽  
Author(s):  
Joseph Pegler ◽  
Jackson Oultram ◽  
Christopher Grof ◽  
Andrew Eamens
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Salt Stress ◽  
Abiotic Stress ◽  
Mirna Target ◽  
Target Gene ◽  
Negative Impact ◽  
Mirna Target Gene ◽  
Target Gene Expression ◽  
Response Phenotype

It is well established among interdisciplinary researchers that there is an urgent need to address the negative impacts that accompany climate change. One such negative impact is the increased prevalence of unfavorable environmental conditions that significantly contribute to reduced agricultural yield. Plant microRNAs (miRNAs) are key gene expression regulators that control development, defense against invading pathogens and adaptation to abiotic stress. Arabidopsis thaliana (Arabidopsis) can be readily molecularly manipulated, therefore offering an excellent experimental system to alter the profile of abiotic stress responsive miRNA/target gene expression modules to determine whether such modification enables Arabidopsis to express an altered abiotic stress response phenotype. Towards this goal, high throughput sequencing was used to profile the miRNA landscape of Arabidopsis whole seedlings exposed to heat, drought and salt stress, and identified 121, 123 and 118 miRNAs with a greater than 2-fold altered abundance, respectively. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) was next employed to experimentally validate miRNA abundance fold changes, and to document reciprocal expression trends for the target genes of miRNAs determined abiotic stress responsive. RT-qPCR also demonstrated that each miRNA/target gene expression module determined to be abiotic stress responsive in Arabidopsis whole seedlings was reflective of altered miRNA/target gene abundance in Arabidopsis root and shoot tissues post salt stress exposure. Taken together, the data presented here offers an excellent starting platform to identify the miRNA/target gene expression modules for future molecular manipulation to generate plant lines that display an altered response phenotype to abiotic stress.

scholarly journals MicroRNA-Mediated Responses to Cadmium Stress in Arabidopsis thaliana

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 130
Author(s):  
Joseph L. Pegler ◽  
Jackson M. J. Oultram ◽  
Duc Quan Nguyen ◽  
Christopher P. L. Grof ◽  
Andrew L. Eamens
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Mirna Target ◽  
Target Gene ◽  
Rna Binding ◽  
Molecular Response ◽  
Cd Stress ◽  
Mirna Target Gene ◽  
Target Gene Expression ◽  
Essential Heavy Metal

In recent decades, the presence of cadmium (Cd) in the environment has increased significantly due to anthropogenic activities. Cd is taken up from the soil by plant roots for its subsequent translocation to shoots. However, Cd is a non-essential heavy metal and is therefore toxic to plants when it over-accumulates. MicroRNA (miRNA)-directed gene expression regulation is central to the response of a plant to Cd stress. Here, we document the miRNA-directed response of wild-type Arabidopsis thaliana (Arabidopsis) plants and the drb1, drb2 and drb4 mutant lines to Cd stress. Phenotypic and physiological analyses revealed the drb1 mutant to display the highest degree of tolerance to the imposed stress while the drb2 mutant was the most sensitive. RT-qPCR-based molecular profiling of miRNA abundance and miRNA target gene expression revealed DRB1 to be the primary double-stranded RNA binding (DRB) protein required for the production of six of the seven Cd-responsive miRNAs analyzed. However, DRB2, and not DRB1, was determined to be required for miR396 production. RT-qPCR further inferred that transcript cleavage was the RNA silencing mechanism directed by each assessed miRNA to control miRNA target gene expression. Taken together, the results presented here reveal the complexity of the miRNA-directed molecular response of Arabidopsis to Cd stress.

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 MicroRNA function can be reversed by altering target gene expression levels

iScience ◽  
2021 ◽  
pp. 103208
Author(s):  
Alexander A. Svoronos ◽  
Stuart G. Campbell ◽  
Donald M. Engelman
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Expression Levels ◽  
Target Gene Expression ◽  
Microrna Function ◽  
Gene Expression Levels

2049-P: The Chd4 Helicase of the Nucleosome Remodeling and Deacetylase Complex Modulates Pdx1 Target Gene Expression In Vitro

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 2049-P
Author(s):  
REBECCA K. DAVIDSON ◽  
NOLAN CASEY ◽  
JASON SPAETH
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Nucleosome Remodeling ◽  
Target Gene Expression
Sign in / Sign up

Export Citation Format

Share Document