scholarly journals The Function of miRNAs in Plants

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 198
Author(s):  
Anthony A Millar
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Circular Rnas ◽  
Messenger Rnas ◽  
Abiotic Stress Response ◽  
Plant Life ◽  
Plant Mirna ◽  
Profile Changes ◽  
Agricultural Impact ◽  
Complementary Binding

MicroRNAs (miRNAs) are a class of small RNAs (sRNAs) that repress gene expression via high complementary binding sites in target mRNAs (messenger RNAs). Many miRNAs are ancient, and their intricate integration into gene expression programs have been fundamental for plant life, controlling developmental programs and executing responses to biotic/abiotic cues. Additionally, there are many less conserved miRNAs in each plant species, raising the possibility that the functional impact of miRNAs extends into virtually every aspect of plant biology. This Special Issue of Plants presents papers that investigate the function and mechanism of miRNAs in controlling development and abiotic stress response. This includes how miRNAs adapt plants to nutrient availability, and the silencing machinery that is responsible for this. Several papers profile changes in miRNA abundances during stress, and another study raises the possibility of circular RNAs acting as endogenous decoys to sequester and inhibit plant miRNA function. These papers act as foundational studies for the more difficult task ahead of determining the functional significance of these changes to miRNA abundances, or the presence of these circular RNAs. Finally, how miRNAs trigger the production of secondary sRNAs is reviewed, along with the potential agricultural impact of miRNAs and these secondary sRNA in the exemplar crop maize.

scholarly journals Regulatory RNAs in Heart Failure

Circulation ◽  
2020 ◽  
Vol 141 (4) ◽  
pp. 313-328 ◽  
Author(s):  
Clarissa Pedrosa da Costa Gomes ◽  
Blanche Schroen ◽  
Gabriela M. Kuster ◽  
Emma L. Robinson ◽  
Kerrie Ford ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Cardiovascular Disease ◽  
Noncoding Rna ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Circular Rnas ◽  
Regulatory Rna ◽  
Messenger Rnas ◽  
Protein Coding

Cardiovascular disease is an enormous socioeconomic burden worldwide and remains a leading cause of mortality and disability despite significant efforts to improve treatments and personalize healthcare. Heart failure is the main manifestation of cardiovascular disease and has reached epidemic proportions. Heart failure follows a loss of cardiac homeostasis, which relies on a tight regulation of gene expression. This regulation is under the control of multiple types of RNA molecules, some encoding proteins (the so-called messenger RNAs) and others lacking protein-coding potential, named noncoding RNAs. In this review article, we aim to revisit the notion of regulatory RNA, which has been thus far mainly confined to noncoding RNA. Regulatory RNA, which we propose to abbreviate as regRNA, can include both protein-coding RNAs and noncoding RNAs, as long as they contribute, directly or indirectly, to the regulation of gene expression. We will address the regulation and functional role of messenger RNAs, microRNAs, long noncoding RNAs, and circular RNAs (ie, regRNAs) in heart failure. We will debate the utility of regRNAs to diagnose, prognosticate, and treat heart failure, and we will provide directions for future work.

Abstract 123: Recently Ruptured Carotid Plaques Have Increased Levels of Circular RNA-16, Which Negatively Regulates the Proproliferative and Antiapoptotic MicroRNA-221: A Novel Mediator of Carotid Plaque Rupture

2014 ◽  
Vol 34 (suppl_1) ◽  
Author(s):  
Hernan A Bazan ◽  
Daniel Lightell ◽  
W Charles Sternbergh ◽  
T Cooper Woods
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Carotid Plaque ◽  
Plaque Rupture ◽  
Rnase H ◽  
Circular Rnas ◽  
Asymptomatic Carotid ◽  
Carotid Plaques ◽  
Vsmc Proliferation ◽  
Symptomatic Carotid

Objectives: Circular RNAs (circRNAs) are dynamically expressed during development and possess binding sites for microRNAs (miRs), small RNAs that negatively regulate gene expression. We recently demonstrated that miR-221, which is associated with VSMC proliferation and inhibition of apoptosis, is decreased in acutely symptomatic carotid plaques. As circRNA-16 possesses binding sites for miR-221 thru seed sequences found within, we hypothesized that circRNA-16 is increased in acutely symptomatic compared to asymptomatic carotid plaques. Methods: Relative changes in gene expression levels of circRNA-16 were compared using a real-time PCR assay and the ΔΔCt method. All samples were run in duplicate; mean/standard error were calculated. One-way ANOVA with Tukey’s test was used to determine significance between groups. Results: Expression of circRNA-16 was confirmed in human VSMC using PCR and resistance to RNAse H. To investigate its role in carotid plaque rupture, levels of circRNA-16 and miR-221 were quantified in patients undergoing urgent CEA for acute neurologic symptoms (n=27), with a mean duration of symptom onset to CEA of 2.4 days, compared to asymptomatic carotid plaques (n=19). In contrast to miR-221, circRNA-16 is increased in the urgent group compared to the asymptomatic carotid plaque group (Figure; 1.51±.26 vs. 1.00±.10, p=.03). Conclusions: We demonstrate circRNA-16 levels are increased and miR-221 levels decreased in acutely ruptured carotid plaques. Furthermore, our data suggest that a circRNA-16/miR-221 axis may be important in fibrous cap degradation and rupture during the transition from a stable to an unstable carotid atherosclerotic plaque.

scholarly journals AFCMEasyModel: An Easy Interface for Modeling Competing Endogenous RNA Networks using ODEs

2017 ◽  
Author(s):  
Mohammad M. Tarek
Keyword(s):  
Gene Expression ◽  
Public Access ◽  
Regulatory Function ◽  
Circular Rnas ◽  
Messenger Rnas ◽  
Competing Endogenous Rna ◽  
Shiny App ◽  
Competing Endogenous Rna Network ◽  
Non Coding Rnas ◽  
User Friendly

AbstractCompeting endogenous RNA networks have been considered to be important regulators of genetic data expression. Circular RNAs and microRNAs interact to form a circular sponge that have been shown to regulate messenger RNAs and hence regulating gene expression. The kinetics by which these non-coding RNAs interact together affecting gene expression are crucial to understand the mechanism of their regulatory function. Herein, we developed AFCMEasyModel as a user-friendly shiny app that enables users to modify regulation parameters of a competing endogenous RNA network based on interaction between circular RNAs and microRNAs in the simulation environment to form a sponge complex. The App provides the source-code for more customized models and allow users to download simulation plots for supplementation of their publications.The App was made available for public-access at: https://mohammadtarek.shinyapps.io/afcmeasymodel/

scholarly journals Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function

2020 ◽  
Vol 22 (1) ◽  
pp. 253
Author(s):  
Venura Herath ◽  
Jeanmarie Verchot
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Functional Groups ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Crop Improvement ◽  
Potato Virus X ◽  
Tissue Growth ◽  
Abiotic Stress Response ◽  
Sequence Alignments

The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil–coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.

scholarly journals CircFAM13B promotes the proliferation of hepatocellular carcinoma by sponging miR-212, upregulating E2F5 expression and activating the P53 pathway

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Xie ◽  
Xiaofeng Hang ◽  
Wensheng Xu ◽  
Jing Gu ◽  
Yuanjing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
In Vivo Studies ◽  
Circular Rnas ◽  
Novel Target ◽  
Underlying Mechanisms

Abstract Background Most of the biological functions of circular RNAs (circRNAs) and the potential underlying mechanisms in hepatocellular carcinoma (HCC) have not yet been discovered. Methods In this study, using circRNA expression data from HCC tumor tissues and adjacent tissues from the Gene Expression Omnibus database, we identified out differentially expressed circRNAs and verified them by qRT-PCT. Functional experiments were performed to evaluate the effects of circFAM13B in HCC in vitro and in vivo. Results We found that circFAM13B was the most significantly differentially expressed circRNA in HCC tissue. Subsequently, in vitro and in vivo studies also demonstrated that circFAM13B promoted the proliferation of HCC. Further studies revealed that circFAM13B, a sponge of miR-212, is involved in the regulation of E2F5 gene expression by competitively binding to miR-212, inhibits the activation of the P53 signalling pathway, and promotes the proliferation of HCC cells. Conclusions Our findings revealed the mechanism underlying the regulatory role played by circFAM13B, miR-212 and E2F5 in HCC. This study provides a new theoretical basis and novel target for the clinical prevention and treatment of HCC.

scholarly journals Study on the Relationship between the miRNA-centered ceRNA Regulatory Network and Fatigue

2021 ◽  
Author(s):  
Xingzhe Yang ◽  
Feng Li ◽  
Jie Ma ◽  
Yan Liu ◽  
Xuejiao Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Hot Spot ◽  
Genetic Research ◽  
Noncoding Rnas ◽  
Messenger Rnas ◽  
Effective Prevention ◽  
Gene Regulatory ◽  
The Relationship

AbstractIn recent years, the incidence of fatigue has been increasing, and the effective prevention and treatment of fatigue has become an urgent problem. As a result, the genetic research of fatigue has become a hot spot. Transcriptome-level regulation is the key link in the gene regulatory network. The transcriptome includes messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). MRNAs are common research targets in gene expression profiling. Noncoding RNAs, including miRNAs, lncRNAs, circRNAs and so on, have been developed rapidly. Studies have shown that miRNAs are closely related to the occurrence and development of fatigue. MiRNAs can regulate the immune inflammatory reaction in the central nervous system (CNS), regulate the transmission of nerve impulses and gene expression, regulate brain development and brain function, and participate in the occurrence and development of fatigue by regulating mitochondrial function and energy metabolism. LncRNAs can regulate dopaminergic neurons to participate in the occurrence and development of fatigue. This has certain value in the diagnosis of chronic fatigue syndrome (CFS). CircRNAs can participate in the occurrence and development of fatigue by regulating the NF-κB pathway, TNF-α and IL-1β. The ceRNA hypothesis posits that in addition to the function of miRNAs in unidirectional regulation, mRNAs, lncRNAs and circRNAs can regulate gene expression by competitive binding with miRNAs, forming a ceRNA regulatory network with miRNAs. Therefore, we suggest that the miRNA-centered ceRNA regulatory network is closely related to fatigue. At present, there are few studies on fatigue-related ncRNA genes, and most of these limited studies are on miRNAs in ncRNAs. However, there are a few studies on the relationship between lncRNAs, cirRNAs and fatigue. Less research is available on the pathogenesis of fatigue based on the ceRNA regulatory network. Therefore, exploring the complex mechanism of fatigue based on the ceRNA regulatory network is of great significance. In this review, we summarize the relationship between miRNAs, lncRNAs and circRNAs in ncRNAs and fatigue, and focus on exploring the regulatory role of the miRNA-centered ceRNA regulatory network in the occurrence and development of fatigue, in order to gain a comprehensive, in-depth and new understanding of the essence of the fatigue gene regulatory network.

Sign in / Sign up

Export Citation Format

Share Document