Neonatal hypoxic-ischemic brain damage (HIBD) is a common factor in neonatal fatalities. miR-126-3p content in cerebral hemorrhage patients is obviously decreased, but its mechanism of action in HIBD is still unclear. The HIBD model was constructed by Rice-Vannucci method, and the change in miR-126-3p was detected. The target genes of miR-126-3p were obtained by database (miRWalk, TargetScan, miRTarbase and miRDB) analysis. The targeting relationship between miR-126-3p and low density lipoprotein receptor related protein (LRP6) was explored based on a dual luciferase assay. miR-126-3p over- and lowexpressed, LRP6 overexpressed and protein kinase C (PKC) pathway agonist phorbol 12-myristate 13-acetate (PMA) were injected into the brains of neonatal rats. The pathological changes in cerebral tissue and neuronal survival were observed by pathological staining. The neurological function was evaluated by foot fault test and wire suspension test. The levels of interleukin (IL)-1beta, IL-6 and tumor necrosis factor-alpha (TNF-alpha) were tested by an ELISA kit. The levels of miR-126-3p, LRP6 and PKC/ERK pathway proteins were tested by qRT-PCR and Western blot. Knockdown of miR-126-3p can aggravate inflammation, brain tissue pathology and neurological impairment in HIBD, while miR-126-3p overexpression can improve it. miR-126-3p can target down-regulate LRP6. miR-126-3p can improve HIBD by down-regulating LRP6 expression and activating the PKC/ERK signaling pathway. miR-126-3p can target down-regulate LRP6 by activating the PKC/ERK signaling pathway to inhibit inflammation in HIBD rats, reduce brain tissue pathology and neurological damage, and improve HIBD. Key words miR-126-3p " LPR6 " PKC/ERK pathway " Hypoxic-ischemic brain damage.

• MeSH
• krysa rodu Rattus MeSH
• LDL receptor related protein 6 * metabolismus   genetika   MeSH
• MAP kinasový signální systém * fyziologie   MeSH
• mikro RNA * genetika   metabolismus   MeSH
• mozková hypoxie a ischemie * metabolismus   patologie   genetika   prevence a kontrola   MeSH
• novorozená zvířata MeSH
• potkani Sprague-Dawley MeSH
• proteinkinasa C * metabolismus   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• LDL receptor related protein 6 * MeSH
• mikro RNA * MeSH
• MIRN126 microRNA, rat MeSH Prohlížeč
• proteinkinasa C * MeSH

MicroRNAs (miRNAs), genome-encoded small RNAs associated with Argonaute proteins, are important negative regulators of gene expression in mammalian cells. miRNAs usually partially base pair with mRNAs, suppress their translation, and destabilize them. Sufficient miRNA abundance is an important factor for efficient target repression. Experimental evidence suggests that oocyte growth causes a dilution effect, which reduces concentrations of maternal miRNAs and renders them functionally inefficient. Consequently, efficient target repression is retained only by those maternal miRNAs which achieve a favorable miRNA:mRNA stoichiometry. Here, we provide protocols for PCR-based quantification of miRNAs and luciferase reporter-based analysis of their activity in mammalian oocytes and early embryos.

• Klíčová slova
• Microinjection, NanoLuc, Oocyte, Zygote, mRNA reporter, miRNAs,
• MeSH
• embryo savčí * metabolismus   MeSH
• mikro RNA * genetika   metabolismus   MeSH
• myši MeSH
• oocyty * metabolismus   MeSH
• polymerázová řetězová reakce metody   MeSH
• reportérové geny MeSH
• vývojová regulace genové exprese * MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• mikro RNA * MeSH

BACKGROUND: Only a limited number of biomarkers guide personalized management of pancreatic neuroendocrine tumors (PanNETs). Transcriptome profiling of microRNA (miRs) and mRNA has shown value in segregating PanNETs and identifying patients more likely to respond to treatment. Because miRs are key regulators of mRNA expression, we sought to integrate expression data from both RNA species into miR-mRNA interaction networks to advance our understanding of PanNET biology. METHODS: We used deep miR/mRNA sequencing on six low-grade/high-risk, well-differentiated PanNETs compared with seven non-diseased tissues to identify differentially expressed miRs/mRNAs. Then we crossed a list of differentially expressed mRNAs with a list of in silico predicted mRNA targets of the most and least abundant miRs to generate high probability miR-mRNA interaction networks. RESULTS: Gene ontology and pathway analyses revealed several miR-mRNA pairs implicated in cellular processes and pathways suggesting perturbed neuroendocrine function (miR-7 and Reg family genes), cell adhesion (miR-216 family and NLGN1, NCAM1, and CNTN1; miR-670 and the claudins, CLDN1 and CLDN2), and metabolic processes (miR-670 and BCAT1/MPST; miR-129 and CTH). CONCLUSION: These novel miR-mRNA interaction networks identified dysregulated pathways not observed when assessing mRNA alone and provide a foundation for further investigation of their utility as diagnostic and predictive biomarkers.

• Klíčová slova
• Biomarkers, MicroRNA, Pancreatic neuroendocrine tumors, mRNA, miR-mRNA interaction networks,
• MeSH
• genové regulační sítě MeSH
• lidé středního věku MeSH
• lidé MeSH
• messenger RNA * genetika   MeSH
• mikro RNA * genetika   MeSH
• nádorové biomarkery genetika   MeSH
• nádory slinivky břišní * genetika   patologie   diagnóza   MeSH
• neuroendokrinní nádory * genetika   patologie   diagnóza   MeSH
• pankreas * metabolismus   patologie   MeSH
• regulace genové exprese u nádorů MeSH
• stanovení celkové genové exprese MeSH
• transkriptom MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• messenger RNA * MeSH
• mikro RNA * MeSH
• nádorové biomarkery MeSH

Ischemic stroke is a leading cause of mortality and long-term disability globally. One of its aspects is the breakdown of the blood-brain barrier (BBB). The disruption of BBB's integrity during stroke exacerbates neurological damage and hampers therapeutic intervention. Recent advances in regenerative medicine suggest that mesenchymal stem cells (MSCs) derived extracellular vesicles (EVs) show promise for restoring BBB integrity. This review explores the potential of MSC-derived EVs in mediating neuroprotective and reparative effects on the BBB after ischemic stroke. We highlight the molecular cargo of MSC-derived EVs, including miRNAs, and their role in enhancing angiogenesis, promoting the BBB and neural repair, and mitigating apoptosis. Furthermore, we discuss the challenges associated with the clinical translation of MSC-derived EV therapies and the possibilities of further enhancing EVs' innate protective qualities. Our findings underscore the need for further research to optimize the therapeutic potential of EVs and establish their efficacy and safety in clinical settings.

• Klíčová slova
• acute ischemic stroke, blood-brain barrier, blood-brain barrier integrity, exosome, extracellular vesicle, mesenchymal stem cell, miRNA, tight junction,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

In RNA interference (RNAi), long double-stranded RNA is cleaved by the Dicer endonuclease into small interfering RNAs (siRNAs), which guide degradation of complementary RNAs. While RNAi mediates antiviral innate immunity in plants and many invertebrates, vertebrates have adopted a sequence-independent response and their Dicer produces siRNAs inefficiently because it is adapted to process small hairpin microRNA precursors in the gene-regulating microRNA pathway. Mammalian endogenous RNAi is thus a rudimentary pathway of unclear significance. To investigate its antiviral potential, we modified the mouse Dicer locus to express a truncated variant (DicerΔHEL1) known to stimulate RNAi and we analyzed how DicerΔHEL1/wt mice respond to four RNA viruses: coxsackievirus B3 and encephalomyocarditis virus from Picornaviridae; tick-borne encephalitis virus from Flaviviridae; and lymphocytic choriomeningitis virus (LCMV) from Arenaviridae. Increased Dicer activity in DicerΔHEL1/wt mice did not elicit any antiviral effect, supporting an insignificant antiviral function of endogenous mammalian RNAi in vivo. However, we also observed that sufficiently high expression of DicerΔHEL1 suppressed LCMV in embryonic stem cells and in a transgenic mouse model. Altogether, mice with increased Dicer activity offer a new benchmark for identifying and studying viruses susceptible to mammalian RNAi in vivo.

In RNA interference (RNAi), the enzyme Dicer cuts long double-stranded RNA into small interfering RNAs that degrade matching RNAs. RNAi is a key antiviral defense in plants and invertebrates but vertebrates evolved a principally different antiviral defense. The authors genetically modified Dicer in mice to activate RNAi in mammals. These modified mice were tested against four RNA viruses but showed no significant antiviral response. However, further increased expression of modified Dicer did suppress one virus (lymphocytic choriomeningitis virus) in embryonic stem cells and in a transgenic mouse model, suggesting that some viruses might be sensitive to increased RNAi activity in mammals.

• MeSH
• DEAD-box RNA-helikasy genetika   metabolismus   MeSH
• malá interferující RNA genetika   MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• přirozená imunita * genetika   MeSH
• ribonukleasa III * genetika   metabolismus   MeSH
• RNA interference * MeSH
• virus encefalomyokarditidy genetika   imunologie   MeSH
• virus lymfocytární choriomeningitidy imunologie   genetika   MeSH
• viry klíšťové encefalitidy genetika   imunologie   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DEAD-box RNA-helikasy MeSH
• Dicer1 protein, mouse MeSH Prohlížeč
• malá interferující RNA MeSH
• ribonukleasa III * MeSH

In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 cells, evident by changes in cell morphology, increased cell proliferation, and oncogenic miRNA expression. Moreover, AGO fPAR-CLIP in Lamin A KO SHSY5Y cells revealed significantly reduced RNAi activity. Further exploration of the nuclear AGO interactome by mass spectrometry identified FAM120A, an RNA-binding protein and known interactor of AGO2. Subsequent FAM120A fPAR-CLIP, revealed that FAM120A co-binds AGO targets and that this competition reduces the RNAi activity. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, FAM120A mediated RNAi impairment, and upregulation of oncogenic miRNAs, facilitating cancer cell proliferation.

• MeSH
• aktivní transport - buněčné jádro MeSH
• Argonaut proteiny * metabolismus   genetika   MeSH
• buněčné jádro * metabolismus   MeSH
• lamin typ A * metabolismus   genetika   MeSH
• lidé MeSH
• melanom genetika   metabolismus   patologie   MeSH
• mikro RNA * metabolismus   genetika   MeSH
• nádorové buněčné linie MeSH
• proliferace buněk * genetika   MeSH
• proteiny vázající RNA metabolismus   genetika   MeSH
• RNA interference * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• AGO2 protein, human MeSH Prohlížeč
• Argonaut proteiny * MeSH
• lamin typ A * MeSH
• mikro RNA * MeSH
• proteiny vázající RNA MeSH

Argonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA 'guide' sequences, and identifies its targets primarily via a 'seed' mediated partial complementarity process. Despite numerous studies, a definitive experimental dataset of AGO2 'guide'-'target' interactions remains elusive. Our study employs two experimental methods-AGO2 CLASH and AGO2 eCLIP, to generate thousands of AGO2 target sites verified by chimeric reads. These chimeric reads contain both the AGO2 loaded small RNA 'guide' and the target sequence, providing a robust resource for modeling AGO2 binding preferences. Our novel analysis pipeline reveals thousands of AGO2 target sites driven by microRNAs and a significant number of AGO2 'guides' derived from fragments of other small RNAs such as tRNAs, YRNAs, snoRNAs, rRNAs, and more. We utilize convolutional neural networks to train machine learning models that accurately predict the binding potential for each 'guide' class and experimentally validate several interactions. In conclusion, our comprehensive analysis of the AGO2 targetome broadens our understanding of its 'guide' repertoire and potential function in development and disease. Moreover, we offer practical bioinformatic tools for future experiments and the prediction of AGO2 targets. All data and code from this study are freely available at https://github.com/ML-Bioinfo-CEITEC/HybriDetector/ .

• MeSH
• Argonaut proteiny genetika   metabolismus   MeSH
• mikro RNA * genetika   metabolismus   MeSH
• RNA ribozomální MeSH
• RNA transferová MeSH
• savci metabolismus   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• Argonaut proteiny MeSH
• mikro RNA * MeSH
• RNA ribozomální MeSH
• RNA transferová MeSH

Juvenile hormone (JH) controls the development and reproduction of insects. Therefore, a tight regulation of the expression of JH biosynthetic enzymes is critical. microRNAs (miRNAs) play significant roles in the post-transcriptional regulation of gene expression by interacting with complementary sequences in target genes. Previously, we reported that several miRNAs were differentially expressed during three developmental stages of Aedes aegypti mosquitoes with different JH levels (no JH, high JH, and low JH). One of these miRNAs was aae-miR-34-5p. In this study, we identified the presence of potential target sequences of aae-miR-34-5p in the transcripts of some genes encoding JH biosynthetic enzymes. We analysed the developmental expression patterns of aae-miR-34-5p and the predicted target genes involved in JH biogenesis. Increases in miRNA abundance were followed, with a delay, by decreases in transcript levels of target genes. Application of an inhibitor and a mimic of aae-miR-34-5p led respectively to increased and decreased levels of thiolase transcripts, which is one of the early genes of JH biosynthesis. Female adult mosquitoes injected with an aae-miR-34-5p inhibitor exhibited significantly increased transcript levels of three genes encoding JH biosynthetic enzymes, acetoacetyl-CoA thiolase (thiolase), farnesyl diphosphate phosphatase, and farnesal dehydrogenase. Overall, our results suggest a potential role of miRNAs in JH production by directly targeting genes involved in its biosynthesis.

• MeSH
• Aedes * MeSH
• juvenilní hormony metabolismus   MeSH
• mikro RNA * genetika   metabolismus   MeSH
• regulace genové exprese MeSH
• zvířata MeSH
• Check Tag
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• juvenilní hormony MeSH
• mikro RNA * MeSH

RNase III Dicer produces small RNAs guiding sequence-specific regulations, with important biological roles in eukaryotes. Major Dicer-dependent mechanisms are RNA interference (RNAi) and microRNA (miRNA) pathways, which employ distinct types of small RNAs. Small interfering RNAs (siRNAs) for RNAi are produced by Dicer from long double-stranded RNA (dsRNA) as a pool of different small RNAs. In contrast, miRNAs have specific sequences because they are precisely cleaved out from small hairpin precursors. Some Dicer homologs efficiently generate both, siRNAs and miRNAs, while others are adapted for biogenesis of one small RNA type. Here, we review the wealth of recent structural analyses of animal and plant Dicers, which have revealed how different domains and their adaptations contribute to substrate recognition and cleavage in different organisms and pathways. These data imply that siRNA generation was Dicer's ancestral role and that miRNA biogenesis relies on derived features. While the key element of functional divergence is a RIG-I-like helicase domain, Dicer-mediated small RNA biogenesis also documents the impressive functional versatility of the dsRNA-binding domain.

• Klíčová slova
• Dicer, dsRBD, helicase, miRNA, siRNA,
• MeSH
• dvouvláknová RNA genetika   MeSH
• malá interferující RNA genetika   metabolismus   MeSH
• mikro RNA * genetika   metabolismus   MeSH
• ribonukleasa III * genetika   MeSH
• RNA interference MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• dvouvláknová RNA MeSH
• malá interferující RNA MeSH
• mikro RNA * MeSH
• ribonukleasa III * MeSH

MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the post-transcriptional regulation of biological processes. miRNAs regulate transcripts through direct binding involving the Argonaute protein family. The exact rules of binding are not known, and several in silico miRNA target prediction methods have been developed to date. Deep learning has recently revolutionized miRNA target prediction. However, the higher predictive power comes with a decreased ability to interpret increasingly complex models. Here, we present a novel interpretation technique, called attribution sequence alignment, for miRNA target site prediction models that can interpret such deep learning models on a two-dimensional representation of miRNA and putative target sequence. Our method produces a human readable visual representation of miRNA:target interactions and can be used as a proxy for the further interpretation of biological concepts learned by the neural network. We demonstrate applications of this method in the clustering of experimental data into binding classes, as well as using the method to narrow down predicted miRNA binding sites on long transcript sequences. Importantly, the presented method works with any neural network model trained on a two-dimensional representation of interactions and can be easily extended to further domains such as protein-protein interactions.

• Klíčová slova
• CLASH, deep learning, interpretation, miRNA target prediction, visualization,
• Publikační typ
• časopisecké články MeSH