miRNA-mediated Regulation Of Gene Expression Research Articles

Genetic variants rs2910164, rs4636297 and rs895819 may contribute to the onset of acute myocardial infarction in Pakistani population.

The most serious type of coronary artery disease (CAD), acute myocardial infarction (AMI), is a major global cause of death. The development of AMI is accompanied by several risk factors. AMI may be caused by variations in the microRNA (miRNA) genes, which have a negative impact on miRNA-mediated regulation of gene expression. The target mRNAs are dysregulated because of these genetic changes in the miRNA genes, which interfere with the vital biological processes that result in AMI. Using allele-specific PCR, the aim of the study is to examine the association of the variants (rs2910164, rs4636297, and rs895819) in MIR146A, MIR126, and MIR27A with AMI susceptibility. A difference in genotype distribution among the patients and control for variation rs2910164 was identified by co-dominant [χ2 = 68.34,2; P value<0.0001], dominant (G/G vs G/C + C/C) [OR = 4.167 (2.860-6.049); P value<0.0001], recessive (C/C vs G/C + G/G) [OR = 0.2584 (0.1798-0.3731); P value<0.0001], and additive models [OR = 3.847 (2.985-4.959); P value<0.0001]. Whereas the association of rs4636297 was investigated by co-dominant [χ2 = 6.882,2; P value = 0.0320], dominant (G/G vs G/A + A/A) [OR = 0.6914 (0.4849-0.9948); P value = 0.0489], recessive (A/A vs A/G + G/G) [OR = 2.434 (0.9849-5.616830); P value = 0.0595], and additive models [OR = 0.7716 (0.6000-0.9918); P value = 0.0433]. Similarly, association of rs895819 was determined by co-dominant [χ2 = 5.277, 2; P value = 0.0715], dominant (G/G vs G/A + A/A) [OR = 1.654(0.9819-2.801); P value = 0.06440], recessive (A/A vs A/G + G/G) [OR = 0.7227 (0.5132-1.022); P value = 0.0748], and additive models [OR = 1.3337 (1.041-1.719); P value = 0.0233]. The results of this study found a significant association of rs2910164 and rs4636297 with AMI and are considered as the risk factor for AMI in the Pakistani population. We observed no significant association of the variant MIR27A (rs895819) with AMI incidence.

Identification of diagnostic biomarkers of gestational diabetes mellitus based on transcriptome gene expression and alternations of microRNAs

&lt;abstract&gt;&lt;sec&gt; &lt;title&gt;Background&lt;/title&gt; &lt;p&gt;Gestational diabetes mellitus (GDM), characterized by glucose intolerance during pregnancy, poses substantial health risks for both mothers and infants due to the interplay of insulin resistance and β-cell dysfunction. Molecular biomarkers, including SNPs, microRNAs (miRNAs), and proteins, have been linked to GDM development during pregnancy. Notably, miRNA-mediated regulation of gene expression holds pivotal roles in metabolic disorders. This study aims to identify diagnostic biomarkers for GDM and establish a diagnostic model.&lt;/p&gt; &lt;/sec&gt;&lt;sec&gt; &lt;title&gt;Methods&lt;/title&gt; &lt;p&gt;Firstly, gene expression data from GDM samples (N = 9) and normal samples (N = 9) were sourced from the Gene Expression Omnibus (GEO) database. Subsequently, the limma package was employed to discern differentially expressed genes (DEGs), with subsequent functional and enrichment analyses executed using the clusterProfiler package. A comprehensive exploration of genes significantly correlated with GDM was undertaken via weighted gene co-expression network analysis (WGCNA). The construction of a protein-protein interaction (PPI) network was facilitated by STRING, while visualization of hub genes was achieved through Cytoscape. Moreover, the miRNA-mRNA network was established using StarBase. Concurrently, immune infiltration significantly correlated with hub genes was identified.&lt;/p&gt; &lt;/sec&gt;&lt;sec&gt; &lt;title&gt;Results&lt;/title&gt; &lt;p&gt;In this study, 209 DEGs between normal and GDM samples were identified, and these genes were associated with collagen containing extracellular matrix heparin binding and axon guidance, etc. Then, 18 modules were identified by WGCNA and the brown module including 212 genes had a significantly negative correlation with GDM (r = −0.66, P = 0.003). Additionally, five low gene expressions (CXCL12, MEF2C, MMP2, SOX17 and THBS2) and two high gene expressions (BMP4 and SFRP5) were identified as GDM related hub genes. Moreover, hub genes regulated by alternations of miRNAs were established and three hub genes (CXCL12, MEF2C and THBS2) were negatively correlated with activated Natural Killer (NK) cells while two hub genes (BMP4 and SFRP5) were positively correlated with activated NK cells.&lt;/p&gt; &lt;/sec&gt;&lt;sec&gt; &lt;title&gt;Conclusions&lt;/title&gt; &lt;p&gt;This study offers novel hub genes that could contribute to the diagnostic approach for GDM, potentially shedding light on the intricate mechanisms underpinning GDM's developmental pathways.&lt;/p&gt; &lt;/sec&gt;&lt;/abstract&gt;

MicroRNA: noncoding but still coding, another example of self-catalysis.

MicroRNAs (miRNAs) are known to interact with specific mRNAs to regulate gene expression at the post-transcriptional level by cleaving/repressing the translation process. MiRNA-mediated regulation of gene expression has become an interesting area of research on biological processes like growth, development, and stress responses. Studies suggest that some of the noncoding RNAs possess short open reading frames (ORFs) that code for micropeptides (miPEPs) having a regulatory function. Dual functions of some MIR genes are being deciphered, wherein the gene is transcribed into a longer transcript having a stem-loop structure and a shorter alternatively spliced transcript with no stem-loop. While the longer transcript is processed into miRNA, the shorter one is translated into miPEP. The miPEP enhances the transcription/production of the pri-miRNA from which it originates. Regulatory action of miPEP being species-specific, synthetic miPEP being is tested for exogenous application on crop plant to improve stress tolerance/agronomic performance. Deployment of the miPEP-mediated regulatory function might be a promising strategy to modulated miRNA-facilitated regulation of gene/trait of interest towards developing climate-resilient crops. In this review, we describe the newly identified and verified function of the MIR gene in the coding of miPEPs along with the comparison of the features of miRNA and miPEP in plant. We also discuss about their potential role in crop improvement and some of the yet unanswered question about miPEP.

Tumor Suppressor microRNAs in Gastrointestinal Cancers: A Mini-Review.

Gastrointestinal (GI) cancer is associated with a group of cancers affecting the organs in the GI tract, with a high incidence and mortality rate. This type of cancer development involves a series of molecular events that arise by the dysregulation of gene expressions and microRNAs (miRNAs). This mini-review focuses on elucidating the mechanism of tumor suppressor miRNA-mediated oncogenic gene silencing, which may contribute to a better understanding of miRNA-mediated gene expression regulation of cell cycle, proliferation, invasion, and apoptosis in GI cancers. In this review, the biological significance of tumor suppressor miRNAs involved in gastrointestinal cancers is briefly explained. The articles were searched with the keywords 'miRNA', 'gastrointestinal cancers', 'esophageal cancer', 'gastric cancer', 'colorectal cancer', 'pancreatic cancer', 'liver cancer', and 'gall bladder cancer' from the Google Scholar and PubMed databases. A total of 71 research and review articles have been collected and referred for this study. This review summarises recent research enhancing the effectiveness of miRNAs as novel prognostic, diagnostic, and therapeutic markers for GI cancer treatment strategies. The expression pattern of various miRNAs has been dysregulated in GI cancers, which are associated with proliferation, cell cycle regulation, apoptosis, migration, and invasion. The role of tumor suppressor miRNAs in the negative regulation of oncogenic gene expression was thoroughly explained in this review. Its potential role as a microRNA therapeutic candidate is also discussed. Profiling and regulating tumor suppressor miRNA expression in gastrointestinal cancers using miRNA mimics could be used as a prognostic, diagnostic, and therapeutic marker, as well as an elucidating molecular therapeutic approach to tumor suppression.

Genetic Variants of MIR27A, MIR196A2 May Impact the Risk for the Onset of Coronary Artery Disease in the Pakistani Population.

Genetic variants in microRNA genes have a detrimental effect on miRNA-mediated regulation of gene expression and may contribute to coronary artery disease (CAD). CAD is the primary cause of mortality worldwide. Several environmental, genetic, and epigenetic factors are responsible for CAD susceptibility. The contribution of protein-coding genes is extensively studied. However, the role of microRNA genes in CAD is at infancy. The study is aimed to investigate the impact of rs895819, rs11614913, and rs2168518 variants in MIR27A, MIR196A2, and MIR4513, respectively, in CAD using allele-specific PCR. Results: For variant rs11614913, significant distribution of the genotypes among the cases and controls was determined by co-dominant [χ2 = 54.4; p value ≤ 0.0001], dominant (C/C vs. C/T + T/T) [OR = 0.257 (0.133–0.496); p value ≤ 0.0001], recessive (T/T vs. C/T + C/C) [OR = 1.56 (0.677–0.632); p value = 0.398], and additive models [OR = 0.421 (0.262–0.675); p value = 0.0004]. Similarly, a significant association of rs895819 was determined by co-dominant [χ2 = 9.669; p value ≤ 0.008], dominant (A/A vs. A/G + G/G) [OR = 0.285 (0.1242–0.6575); p value ≤ 0.0034], recessive (G/G vs. A/G + A/A) [OR = 0.900 (0.3202–3.519); p value = 1.000], and additive models [OR = 0.604 (0.3640–1.002); p value = 0.05] while no significant association of rs2168518 with CAD was found. Conclusion: The variants rs895819 and rs11614913 are the susceptibility factors for CAD.

The miRNome of Depression.

Depression is an effect of complex interactions between genetic, epigenetic and environmental factors. It is well established that stress responses are associated with multiple modest and often dynamic molecular changes in the homeostatic balance, rather than with a single genetic factor that has a strong phenotypic penetration. As depression is a multifaceted phenotype, it is important to study biochemical pathways that can regulate the overall allostasis of the brain. One such biological system that has the potential to fine-tune a multitude of diverse molecular processes is RNA interference (RNAi). RNAi is an epigenetic process showing a very low level of evolutionary diversity, and relies on the posttranscriptional regulation of gene expression using, in the case of mammals, primarily short (17–23 nucleotides) noncoding RNA transcripts called microRNAs (miRNA). In this review, our objective was to examine, summarize and discuss recent advances in the field of biomedical and clinical research on the role of miRNA-mediated regulation of gene expression in the development of depression. We focused on studies investigating post-mortem brain tissue of individuals with depression, as well as research aiming to elucidate the biomarker potential of miRNAs in depression and antidepressant response.

MicroRNAs Instruct and Maintain Cell Type Diversity in the Nervous System.

Characterizing the diverse cell types that make up the nervous system is essential for understanding how the nervous system is structured and ultimately how it functions. The astonishing range of cellular diversity found in the nervous system emerges from a small pool of neural progenitor cells. These progenitors and their neuronal progeny proceed through sequential gene expression programs to produce different cell lineages and acquire distinct cell fates. These gene expression programs must be tightly regulated in order for the cells to achieve and maintain the proper differentiated state, remain functional throughout life, and avoid cell death. Disruption of developmental programs is associated with a wide range of abnormalities in brain structure and function, further indicating that elucidating their contribution to cellular diversity will be key to understanding brain health. A growing body of evidence suggests that tight regulation of developmental genes requires post-transcriptional regulation of the transcriptome by microRNAs (miRNAs). miRNAs are small non-coding RNAs that function by binding to mRNA targets containing complementary sequences and repressing their translation into protein, thereby providing a layer of precise spatial and temporal control over gene expression. Moreover, the expression profiles and targets of miRNAs show great specificity for distinct cell types, brain regions and developmental stages, suggesting that they are an important parameter of cell type identity. Here, we provide an overview of miRNAs that are critically involved in establishing neural cell identities, focusing on how miRNA-mediated regulation of gene expression modulates neural progenitor expansion, cell fate determination, cell migration, neuronal and glial subtype specification, and finally cell maintenance and survival.

Selection and validation of reference genes for qPCR analysis of miRNAs and their targets during somatic embryogenesis in tamarillo (Solanum betaceum Cav.)

Quantitative reverse transcriptase PCR is a powerful tool for precise gene expression quantification. Using suitable reference genes is crucial for a proper normalization and interpretation of results, particularly in dynamic transcriptional networks with the involvement of several miRNAs and their targets, such as somatic embryogenesis (SE). Here, we aimed to identify genes to be used as internal controls for quantitative detection of miRNAs and mRNAs during the SE process in Solanum betaceum. The expression of EF1α, GAPDH, ACT, UBQ10, Fe-SOD, U6, snoR14, miR159a, miR162 and miR166a was tested in nine time-points of the SE process, particularly during induction, embryo development and conversion. Analyses of transcriptional stability were performed using RefFinder tool that integrates geNorm, NormFinder, BestKeeper and Delta-Ct algorithms. Among these candidates, Fe-SOD, ACT and U6 emerged consistently as the most suitable to normalize gene expression, whereas miR166a was the most appropriate for normalization in calli samples. In order to validate these results, expression of miR396 and GRF1 was quantified and normalized with the most and the least stable genes and also with the most stable miRNA. Fe-SOD + ACT revealed to be the optimal combination for precise quantification of miRNA-mediated regulation of gene expression during SE in tamarillo. Fe-SOD + ACT is the most suitable combination of reference genes for RT-qPCR normalization and accurate quantification of miRNAs and their targets during tamarillo somatic embryogenesis induction, embryo development and conversion stages.

Association of Genetic Variation in the 3'UTR of LHX6, IMMP2L, and AADAC With Tourette Syndrome.

Background: Tourette Syndrome (TS) is a neurodevelopmental disorder that presents with motor and vocal tics early in childhood. The aim of this study was to investigate genetic variants in the 3' untranslated region (3'UTR) of TS candidate genes with a putative link to microRNA (miRNA) mediated regulation or gene expression.Methods: We used an in silico approach to identify 32 variants in the 3'UTR of 18 candidate genes putatively changing the binding site for miRNAs. In a sample composed of TS cases and controls (n = 290), as well as TS family trios (n = 148), we performed transmission disequilibrium test (TDT) and meta-analysis.Results: We found positive association of rs3750486 in the LIM homeobox 6 (LHX6) gene (p = 0.021) and rs7795011 in the inner mitochondrial membrane peptidase subunit 2 (IMMP2L) gene (p = 0.029) with TS in our meta-analysis. The TDT showed an over-transmission of the A allele of rs1042201 in the arylacetamide deacetylase (AADAC) gene in TS patients (p = 0.029).Conclusion: This preliminary study provides further support for the involvement of LHX6, IMMP2L, and AADAC genes, as well as epigenetic mechanisms, such as altered miRNA mediated gene expression regulation in the etiology of TS.

Differential miRNA-Gene Expression in M Cells in Response to Crohn's Disease-Associated AIEC.

Adherent-invasive Escherichia coli (AIEC), which abnormally colonize the ileal mucosa of Crohn’s disease (CD) patients, are able to invade intestinal epithelial cells (IECs) and translocate through M cells overlying Peyer’s patches. The levels of microRNA (miRNA) and gene expression in IECs and M cells upon AIEC infection have not been investigated. Here, we used human intestinal epithelial Caco-2 monolayers and an in vitro M-cell model of AIEC translocation to analyze comprehensive miRNA and gene profiling under basal condition and upon infection with the reference AIEC LF82 strain. Our results showed that AIEC LF82 translocated through M cells but not Caco-2 monolayers. Both differential gene expression and miRNA profile in M cells compared to Caco-2 cells were obtained. In addition, AIEC infection induces changes in gene and miRNA profiles in both Caco-2 and M cells. In silico analysis showed that certain genes dysregulated upon AIEC infection were potential targets of AIEC-dysregulated miRNAs, suggesting a miRNA-mediated regulation of gene expression during AIEC infection in Caco-2, as well as M cells. This study facilitates the discovery of M cell-specific and AIEC response-specific gene-miRNA signature and enhances the molecular understanding of M cell biology under basal condition and in response to infection with CD-associated AIEC.

Modulators of MicroRNA Function in the Immune System.

MicroRNAs (miRNAs) play a key role in fine-tuning host immune homeostasis and responses through the negative regulation of mRNA stability and translation. The pathways regulated by miRNAs are well characterized, but the precise mechanisms that control the miRNA-mediated regulation of gene expression during immune cell-development and immune responses to invading pathogens are incompletely understood. Context-specific interactions of miRNAs with other RNA species or proteins may modulate the function of a given miRNA. Dysregulation of miRNA function is associated with various human diseases, such as cardiovascular diseases and cancers. Here, we review the potential modulators of miRNA function in the immune system, including the transcription regulators of miRNA genes, miRNA-processing enzymes, factors affecting miRNA targeting, and intercellular communication.

Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family

BackgroundPlant NADPH oxidase (NOX), also known as respiratory burst oxidase homolog (rboh), encoded by the rboh gene, is a key enzyme in the reactive oxygen species (ROS) metabolic network. It catalyzes the formation of the superoxide anion (O2•−), a type of ROS. In recent years, various studies had shown that members of the plant rboh gene family were involved in plant growth and developmental processes as well as in biotic and abiotic stress responses, but little is known about its functional role in upland cotton.ResultsIn the present study, 26 putative Ghrboh genes were identified and characterized. They were phylogenetically classified into six subfamilies and distributed at different densities across 18 of the 26 chromosomes or scaffolds. Their exon-intron structures, conserved domains, synteny and collinearity, gene family evolution, regulation mediated by cis-acting elements and microRNAs (miRNAs) were predicted and analyzed. Additionally, expression profiles of Ghrboh gene family were analyzed in different tissues/organs and at different developmental stages and under different abiotic stresses, using RNA-Seq data and real-time PCR. These profiling studies indicated that the Ghrboh genes exhibited temporal and spatial specificity with respect to expression, and might play important roles in cotton development and in stress tolerance through modulating NOX-dependent ROS induction and other signaling pathways.ConclusionsThis comprehensive analysis of the characteristics of the Ghrboh gene family determined features such as sequence, synteny and collinearity, phylogenetic and evolutionary relationship, expression patterns, and cis-element- and miRNA-mediated regulation of gene expression. Our results will provide valuable information to help with further gene cloning, evolutionary analysis, and biological function analysis of cotton rbohs.

Incidence of MicroR-4513C/T Gene Variability in Coronary Artery Disease - A Case-Control Study.

Genetic variants in pre-microRNA genes or the 3'UTR of miRNA target genes could influence miRNA-mediated regulation of gene expression and thus contribute to the susceptibility and prognosis of human diseases. Several studies have investigated the association of genetic variants in the seed region of miRNAs with cardiometabolic phenotypes .Therefore the aim of study was to investigate the potential association of miR-4513 rs2168518 C>T gene variability with the risk of developing CAD and its association with different cardiometabolic phenotypes in an Indian cohort to stratify CAD burden in the general population. The study was conducted on 100 clinically confirmed CAD patients and 100 healthy individuals. Genotyping of MicroR-4513 rs2168518C>T gene variability was performed using Amplification refractory mutation system PCR method. A significant difference was observed in the genotype distribution among CAD cases and healthy controls. The frequencies of three genotypes CC, CT, TT in CAD patient and healthy controls were 5%, 77%, 18%, and 28%, 45% and 27% respectively. A multivariate analysis showed that miR- 4513 rs2168518 polymorphism is associated with an increased susceptibility to CAD in codominant inheritance model for variant CC vs. CT OR 9.58 CI (3.45-26.57), RR 2.3(1.75-3.02), P=0.001. Results also indicate a potential dominant effect of miR-4513 rs2168518 C/T polymorphism on susceptibility of CAD in dominant inheritance model for variant CC vs. (CT+TT) OR 7.38 (2.71-20.07), RR 1.96 (1.56-2.46), P=0.001. In allelic comparison, T allele weakly increased risk of CAD compared to C allele (OR=1.50, 95% CI (1.09-2.26) RR 1.15 (0.94-1.39) P=0.044. It is concluded that CT genotype and T allele of microR-4513 rs2168518 is strongly associated with increased susceptibility to CAD. Furthers studies with larger sample sizes are necessary to confirm this result.

49-OR: Association of Gene Polymorphisms and Plasma MiRNAs with Diabetic Retinopathy

Circulating microRNAs (miRNAs/miRs) have emerged as potential disease biomarkers; however, their expression in diabetic retinopathy (DR) has been evaluated only recently in humans. Whilst it is recognized that sequence variants in miRNA genes (miRSNPs) can alter the miRNA-mediated regulation of gene expression, there are almost no studies on the association of miRSNPs with DR. In this case-control study, we investigated whether the functional polymorphisms rs531564 G&amp;gt;C (MIR124-1), rs4636297 A&amp;gt;G (MIR126) and 2910164 C&amp;gt;G (MIR146A) are associated with DR in 1,025 Brazilians with type 2 diabetes. We also evaluated whether the plasma levels of miR-124, miR-126 and miR-146a are associated with DR and with miRSNPs in 182 patients. Blood donors were included to determine the prevalence of miRSNPs (n = 104) and miRNA expression (n = 20) in the general population. Genotyping was done by real-time PCR and plasma levels were quantified by RT-qPCR. Genotype and allele frequencies in diabetic subjects did not significantly differ from those of blood donors, and the minor allele frequencies were similar to those reported in other populations. The MIR126 heterozygous genotype was more frequent in patients without DR than in those with DR (52% versus 44%, respectively, p = 0.040), and remained associated with this complication after controlling for clinical covariates. MiR-126 was markedly downregulated in diabetic subjects as compared to blood donors and even more reduced among those with DR (mean log2 fold-change of -0.7 ± 1.7, -1.1 ± 2.0 and -1.7 ± 1.6 for subjects without DR, with nonproliferative DR or with proliferative DR, p = 0.002). Patients carrying the A allele of the rs4636297 polymorphism had almost twice higher levels of miR-126 than patients with GG genotype. MiR-126 and miR-146a were strongly correlated and the levels of miR-146a were also lower in diabetic subjects than in blood donors. Overall, our findings reinforce that gene variants and expression of miRNAs are associated with DR in type 2 diabetes. Disclosure E.R. Polina: None. R.C. Sbruzzi: None. F.M. de Oliveira: None. D. Crispim: None. M.D. Enoia: None. L.H. Canani: Research Support; Self; Novo Nordisk Inc. Speaker's Bureau; Self; Boehringer Ingelheim Pharmaceuticals, Inc., Sanofi. K.G. Santos: None. Funding Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (1994-2551/13-4); Fundo de Incentivo à Pesquisa e Eventos do Hospital de Clínicas de Porto Alegre (14-0645)

MiRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga Chlamydomonas reinhardtii.

MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation-small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.

Prediction of Plant miRNA Targets.

microRNAs (miRNAs) are the central component of an important layer of regulation of gene expression at posttranscriptional level. In plants, miRNAs target the transcripts in a highly complementary sequence-dependent manner. Extensive research is being made to study genome-wide miRNA-mediated regulation of gene expression, which has resulted in the development of many tools for in silico prediction of miRNA targets. Although several tools have been developed for predicting miRNA targets in model plants, genome-wide analysis of miRNA targets is still a challenge for non-model species that lack dedicated tools. Here, we describe an in silico procedure for studying miRNA-mediated interactions in plants, which is based on the fact that canonical miRNA-target sites are highly complementary, the miRNAs negatively regulate the expression of their target genes, and miRNAs may form regulatory networks as one miRNA may target more than one transcript and vice versa to modulate and fine-tune expression of the genome.

M115 - ASSOCIATION OF THE PLCB1 GENE WITH DRUG DEPENDENCE

Background Drug dependence is a complex neuropsychiatric disorder that results from the interaction of genetic and environmental factors. MicroRNAs (miRNAs) are very abundant in the central nervous system and seem to play key roles in the drug-induced plasticity of the brain that likely drives the emergence of addiction. Some studies suggest that SNPs located in both miRNAs and miRNA target sites may alter the miRNA-mediated regulation of gene expression that underlies disease and non-pathological phenotypes. Here we aimed at exploring the role of miRNAs in drug addiction by performing a two stage case-control association study. Methods We genotyped SNPs located in regions of miRNA binding in a Spanish sample of 735 cases and 739 controls and replicated the results in an independent follow-up sample of 663 cases and 667 controls. The possible functional impact of associated SNPs on the binding of different miRNAs was performed with a luciferase reporter assay. Finally, we evaluated alterations of gene expression under cocaine in a gene harboring associated variants using different in vivo and in vitro models. Results We identified an association between rs1047383 in the 3’UTR of the PLCB1 gene and drug dependence, particularly with cocaine addiction, that was replicated. Then we tested the effect of this SNP and rs1047381-rs708910 (in LD with it) on the binding of 10 miRNAs. Hsa-miR-582 was found to downregulate gene expression, without showing differences between the two alleles at rs708910. Finally, we explored the possibility that PLCB1 expression is altered by cocaine. We observed a significant upregulation of PLCB1 in the nucleus accumbens of cocaine abusers and in human dopaminergic-like neurons after cocaine treatment. In order to confirm the contribution of PLCB1 to cocaine dependence we are currently assessing cocaine-seeking behavior in heterozygous Plcb1 knockout mice. Discussion To our knowledge, this is the first study assessing the effect of SNPs in miRNA binding sites in drug dependence, and we provide additional evidence for the participation of the PLCB1 gene in the vulnerability to susceptibility to drug dependence.

Dicer promotes endothelial recovery and limits lesion formation after vascular injury through miR-126-5p

BackgroundThe recovery of endothelial cells (ECs) after vascular injury is mainly mediated by the proliferation of resident ECs, thereby reducing neointima formation. The RNase Dicer processes microRNAs (miRNAs) and regulates EC function by controlling miRNA-mediated regulation of gene expression. This study aimed to investigate the impact of miRNA biogenesis in ECs on endothelial repair during lesion formation after vascular injury. Methods and resultsTo study the effect of Dicer on ECs during neointima formation, conditional deletion of Dicer was induced in Apoe−/− mice (EC-Dicerflox) by tamoxifen injection. Following wire-induced injury to carotid arteries of EC-Dicerflox mice, the EC recovery was impaired and the neointima formation and lesional macrophage accumulation was increased. Moreover, conditional deletion of Dicer in ECs diminished the expression of miR-126-5p in EC-Dicerflox mice. Notably, reconstitution of miR-126-5p in the injured arteries of EC-Dicerflox mice using miR-126-5p mimic, prevented the impaired endothelial recovery and increased lesion formation observed in EC-Dicerflox mice. ConclusionsDeficiency of endothelial Dicer diminished endothelial recovery and promoted neointima formation probably due to impaired miR-126-5p expression. Treatment with miR-126-5p mimics promotes endothelial recovery and thereby limits neointima formation. Thus, miR-126-5p therapy represents a potential approach to improve endothelial recovery and prevent restenosis following vascular injury.

Intronic miRNA mediated gene expression regulation controls protein crowding inside the cell

Gene regulatory effects of microRNAs at a posttranscriptional level have been established over the last decade. In this study, we analyze the interaction networks of mRNA translation regulation through intronic miRNA, under various tissue-specific cellular contexts, taking into account the thermodynamic affinity, chemical kinetics, co-localization, concentration levels, network parameters and the presence of competitive interactors. This database, and analysis has been made available through an open-access web-server, miRiam, to promote further exploration. Here we report that expression of genes involved in Apoptosis Processes, Immune System Processes, Translation Regulator Activities, and Molecular Transport Activities within the cell are predominately regulated by miRNA mediation. Our findings further indicate that this regulatory effect has a profound effect in controlling protein crowding inside the cell. A miRNA mediated gene expression regulation serves as a temporal regulator, allowing the cellular machinery to temporarily ‘pause’ the translation of mRNA, indicating that the miRNA–mRNA interactions may be important for governing the optimal usage of cell volume.

Expansion of Capsicum annuum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles.

Small regulatory RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) have emerged as important transcriptional and post-transcriptional regulators controlling a wide variety of physiological processes including fruit development. Data are, however, limited for their potential roles in developmental processes determining economically important traits of crops. The current study aimed to discover and characterize differentially expressed miRNAs and siRNAs in sweet pepper (Capsicum annuum) during fruit expansion. High-throughput sequencing was employed to determine the small regulatory RNA expression profiles in various fruit tissues, such as placenta, seed, and flesh at 28 and 40 days after anthesis. Comparative differential expression analyses of conserved, already described and our newly predicted pepper-specific miRNAs revealed that fruit expansion is accompanied by an increasing level of miRNA-mediated regulation of gene expression. Accordingly, ARGONAUTE1 protein, the primary executor of miRNA-mediated regulation, continuously accumulated to an extremely high level in the flesh. We also identified numerous pepper-specific, heterochromatin-associated 24-nt siRNAs (hetsiRNAs) which were extremely abundant in the seeds, as well as 21-nt and 24-nt phased siRNAs (phasiRNAs) that were expressed mainly in the placenta and the seeds. This work provides comprehensive tissue-specific miRNA and siRNA expression landscape for a developing pepper fruit. We identified several novel, abundantly expressing tissue- and pepper-specific small regulatory RNA species. Our data show that fruit expansion is associated with extensive changes in sRNA abundance, raising the possibility that manipulation of sRNA pathways may be employed to improve the quality and quantity of the pepper fruit.