Regulation of mRNA Translation and Stability by microRNAs

The importance of hsa-miR-28 in human malignancies

MicroRNA production in tumorigenesis is dysregulated by a variety of processes, such as proliferation and removal of microRNA genes, aberrant transcriptional regulation of microRNAs, disrupted epigenetic alterations, and failures in the miRNA biogenesis machinery. Under some circumstances, miRNAs may act as tumorigenic and maybe anti-oncogenes. Tumor aspects such as maintaining proliferating signals, bypassing development suppressors, delaying apoptosis, stimulating metastasis and invasion, and promoting angiogenesis have been linked to dysfunctional and dysregulated miRNAs. MiRNAs have been found as possible biomarkers for human cancer in a great deal of research, which requires additional evaluation and confirmation. It is known that hsa-miR-28 can function as an oncogene or tumor suppressor in many malignancies, and it does this by modulating the expression of several genes and the downstream signaling network. MiR-28-5p and miR-28-3p, which originate from the same RNA hairpin precursor miR-28, have essential roles in a variety of cancers. This review outlines the function and mechanisms of miR-28-3p and miR-28-5p in human cancers and illustrates the miR-28 family's potential utility as a diagnostic biomarker for prognosis and early detection of cancers.

CircRNA hsa_circ_0006859 inhibits the osteogenic differentiation of BMSCs and aggravates osteoporosis by targeting miR-642b-5p/miR-483-3p and upregulating EFNA2/DOCK3

Hsa_circ_0006859 has been found as a possible biomarker for postmenopausal osteoporosis (PMOP) with an effect on the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs), but the underlying mechanism is unclear. Bioinformatics analysis was used to identify dysregulated RNAs involved in osteoporosis based on public datasets. Function assays were used to determine the functions of hsa_circ_0006859 on cell proliferation and osteogenic differentiation in vitro. It was found that hsa_circ_0006859 was upregulated in OVX mice-derived BMSCs, but lowly expressed during osteogenic differentiation. Overexpressing hsa_circ_0006859 inhibited the cell proliferation and osteogenesis of BMSCs and hFOB 1.19 cells, vice versa. Bilateral ovariectomy (OVX) was used to induce PMOP in mice. The interactions among circ_0006859, miR-642b-5p/miR-483-3p, and EFNA2/DOCK3 were determined using the RIP assay. Silencing circ_0006859 relieved PMOP in mice. Mechanistically, circ_0006859 bound to miR-642b-5p/miR-483-3p directly, while miR-642b-5p and miR-483-3p respectively targeted EFNA2 and DOCK3. Hsa_circ_0006859 downregulated the expression of miR-642b-5p/miR-483-3p to upregulate EFNA2/DOCK3. Additionally, miR-642b-5p/miR-483-3p targeted EFNA2/DOCK3 to inhibit BMSCs osteogenic differentiation and facilitate osteoporosis progression by inactivating the Wnt signaling. In conclusion, hsa_circ_0006859 is involved in PMOP by targeting miR-642b-5p/EFNA2 and miR-483-3p/DOCK3 axes to maintain the Wnt-signaling pathway, which may be a novel possible therapeutic targets and biomarkers for PMOP.

CircHSPG2 knockdown attenuates hypoxia-induced apoptosis, inflammation, and oxidative stress in human AC16 cardiomyocytes by regulating the miR-1184/MAP3K2 axis

Circular RNAs (circRNAs) have been identified as vital regulators in cardiovascular diseases, including acute myocardial infarction (AMI). In this study, the function and mechanism of circRNA heparan sulfate proteoglycan 2 (circHSPG2) in hypoxia-induced injury in AC16 cardiomyocytes were investigated. AC16 cells were stimulated with hypoxia to establish an AMI cell model in vitro. Real-time quantitative PCR and western blot assays were performed to quantify the expression levels of circHSPG2, microRNA-1184 (miR-1184), and mitogen-activated protein kinase kinase kinase 2 (MAP3K2). Counting Kit-8 (CCK-8) assay was used to measure cell viability. Flow cytometry was performed to detect cell cycle and apoptosis. Enzyme-linked immunosorbent assay (ELISA) was used to determine the expression of inflammatory factors. Dual-luciferase reporter, RNA immunoprecipitation (RIP), and RNA pull-down assays were used to analyze the relationship between miR-1184 and circHSPG2 or MAP3K2. In AMI serum, circHSPG2 and MAP3K2 mRNA were highly expressed and miR-1184 was down-regulated. Hypoxia treatment elevated HIF1α expression and repressed cell growth and glycolysis. Moreover, hypoxia promoted cell apoptosis, inflammation, and oxidative stress in AC16 cells. Hypoxia-induced circHSPG2 expression in AC16 cells. CircHSPG2 knockdown alleviated hypoxia-induced AC16 cell injury. CircHSPG2 directly targeted miR-1184, and miR-1184 targeted and suppressed MAP3K2. Inhibition of miR-1184 or overexpression of MAP3K2 abolished the alleviated effect of circHSPG2 knockdown on hypoxia-induced AC16 cell injury. Overexpression of miR-1184 relieved hypoxia-induced impairment in AC16 cells by MAP3K2. CircHSPG2 could regulate MAP3K2 expression through miR-1184. CircHSPG2 knockdown protected AC16 cells from hypoxia-induced injury by regulating the miR-1184/MAP3K2 cascade.

CircTNPO3 promotes hepatocellular carcinoma progression by sponging miR-199b-5p and regulating STRN expression

Hepatocellular carcinoma (HCC) is the most common primary liver tumor, which seriously threatens human health. CircTNPO3 was up-regulated in HCC tissues. However, the regulatory mechanism of circTNPO3 in HCC was still unclear. We aimed to investigate the circTNPO3 function in the development of HCC. qRT-PCR and Western blot examined gene and protein levels. CCK8, EdU, flow cytometry, and Transwell assays were used to detect cell viability, proliferation, apoptosis, and invasion abilities. Dual-luciferase reporter and RIP assays determined the relationship between circTNPO3, miR-199b-5p, and striatin (STRN). The effect of CircTNPO3 on HCC progress was investigated in vivo. CircTNPO3 and STRN were significantly increased, while miR-199b-5p was repressed in HCC tissues or cells. Afterward, miR-199b-5p was negatively correlated with STRN. circTNPO3 was positively correlated with STRN. Knockdown of circTNPO3 inhibited cell viability, proliferation, invasion, and promoted apoptosis, while circTNPO3 overexpression had the opposite results. Furthermore, miR-199b-5p inhibition could eliminate the regulatory effect of sh-circTNPO3 on the proliferation and apoptosis in HCC cells. CircTNPO3 positively regulated STRN expression by targeting miR-199b-5p. MiR-199b-5p suppressed HCC progression by inhibiting STRN expression. Tumor formation in nude mice showed that knockdown of circTNPO3 significantly inhibited tumor growth and suppressed ki-67 levels. CircTNPO3 promoted HCC progression through regulating STRN expression by sponging miR-199b-5p, which provided a strategy for HCC treatment.

Long non-coding RNAs in retinal neovascularization: current research and future directions

PURPOSE

Retinal neovascularization (RNV) is an intractable pathological hallmark of numerous ocular blinding diseases, including diabetic retinopathy, retinal vein occlusion, and retinopathy of prematurity. However, current therapeutic methods have potential side effects and limited efficacy. Thus, further studies on the pathogenesis of RNV-related disorders and novel therapeutic targets are critically required. Long non-coding RNAs (lncRNAs) have various functions and participate in almost all biological processes in living cells, such as translation, transcription, signal transduction, and cell cycle control. In addition, recent research has demonstrated critical modulatory roles of various lncRNAs in RNV. In this review, we summarize current knowledge about the expression and regulatory functions of lncRNAs related to the progression of pathological RNV.

METHODS

We searched databases such as PubMed and Web of Science to gather and review information from the published literature.

CONCLUSIONS

In general, lncRNA MEG3 attenuates RNV, thus protecting the retina from excessive and dysregulated angiogenesis under high glucose stress. In contrast, lncRNAs MALAT1, MIAT, ANRIL, HOTAIR, HOTTIP, and SNHG16, have been identified as causative molecules in the pathological progression of RNV. Comprehensive and in-depth studies of the roles of lncRNAs in RNV indicate that targeting lncRNAs may be an alternative therapeutic approach in the near future, enabling new options for attenuating RNV progression and treating RNV-related retinal diseases.

Establishment of a schizophrenia classifier based on peripheral blood signatures and investigation of pathogenic miRNA-mRNA regulation

To date, the diagnosis of schizophrenia (SCZ) mainly relies on patients' or guardians' self-reports and clinical observation, and the pathogenesis of SCZ remains elusive. In this study, we sought to develop a reliable classifier for diagnosing SCZ patients and provide clues to the etiology and pathogenesis of SCZ. Based on the high throughput sequencing analysis of peripheral blood miRNA expression profile and weighted gene co-expression network analysis (WGCNA) in our previous study, we selected eleven hub miRNAs for validation by qRT-PCR in 51 SCZ patients and 51 controls. miR-939-5p, miR-4732-3p let-7d-3p, and miR-142-3p were confirmed to be significantly up-regulated, and miR-30e-3p and miR-23a-3p were down-regulated in SCZ patients. miR-30e-3p with the most considerable fold change and statistically significance was selected for targeting validation. We first performed bioinformatics prediction followed by qRT-PCR and verified the up-regulation of potential target mRNAs (ABI1, NMT1, HMGB1) expression. Next, we found that the expression level of ABI1 was significantly up-regulated in SH-SY5Y cells transfected with miR-30e-3p mimics. Lastly, we conducted a luciferase assay in 293T cells confirming that miR-30e-3p could directly bind with the 3'untranslated region (3'-UTR) of ABI1, revealing that miR-30e-3p might play a role in the polymerization of neuronal actin and the reconstruction of the cytoskeleton via the downstream regulation of ABI1. In addition, we constructed a classifier by a series of bioinformatics algorithms and evaluated its diagnostic performance. It appears that the classifier consists of miRNAs and mRNAs possess a better discrimination performance than individual miRNA or mRNA in SCZ.

Molecular characterization of extracellular vesicles derived from follicular fluid of women with and without PCOS: integrating analysis of differential miRNAs and proteins reveals vital molecules involving in PCOS

PURPOSE

To elucidate the characterization of extracellular vesicles (EVs) in the follicular fluid-derived extracellular vesicles (FF-EVs) and discover critical molecules and signaling pathways associating with the etiology and pathobiology of PCOS, the differentially expressed miRNAs (DEmiRNAs) and differentially expressed proteins profiles (DEPs) were initially explored and combinedly analyzed.

METHODS

First, the miRNA and protein expression profiles of FF-EVs in PCOS patients and control patients were compared by RNA-sequencing and tandem mass tagging (TMT) proteomic methods. Subsequently, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used to analyze the biological function of target genes of DEmiRNAs and DEPs. Finally, to discover the functional miRNA-target gene-protein interaction pairs involved in PCOS, DEmiRs target gene datasets and DEPs datasets were used integratedly.

RESULTS

A total of 6 DEmiRNAs and 32 DEPs were identified in FF-EVs in patients with PCOS. Bioinformatics analysis revealed that DEmiRNAs target genes are mainly involved in thiamine metabolism, insulin secretion, GnRH, and Apelin signaling pathway, which are closely related to the occurrence of PCOS. DEPs also closely related to hormone metabolism processes such as steroid hormone biosynthesis. In the analysis integrating DEmiRNAs target genes and DEPs, two molecules, GRAMD1B and STPLC2, attracted our attention that are closely associated with cholesterol transport and ceramide biosynthesis, respectively.

CONCLUSION

Dysregulated miRNAs and proteins in FF-EVs, mainly involving in hormone metabolism, insulin secretion, neurotransmitters regulation, adipokine expression, and secretion, may be closely related to PCOS. The effects of GRAMD1B and STPLC2 on PCOS deserve further study.

Dexmedetomidine alleviates myocardial ischemia-reperfusion injury by down-regulating miR-34b-3p to activate the Jagged1/Notch signaling pathway

BACKGROUND

Myocardial ischemia/reperfusion (I/R) injury is a fatal event that usually occurs after reperfusion therapy for myocardial infarction. Dexmedetomidine (Dex) has been shown to be beneficial in the treatment of myocardial infarction, however, its underlying mechanism for regulating I/R injury is unclear.

METHODS

H9c2 cell and rat models of I/R injury were established via oxygen-glucose deprivation reoxygenation (OGD/R) and occlusion of the left anterior descending branch of coronary artery, respectively. Flow cytometry, MTT, or DHE assay detected cell activity, ROS, or apoptosis, respectively. The expression levels of miR-34b-3p and related mRNAs were determined using qRT-PCR. Related protein expression levels were detected by Western blotting and ELISA test. The interaction between miR-34b-3p and Jagged1 was assessed by dual luciferase reporter and RIP assays. The morphology of cardiac tissue was examined by TTC, HE, and TUNEL labeling.

RESULTS

Dex markedly inhibited the inflammatory damage and apoptosis caused by OGD/R in H9c2 cells. MiR-34b-3p and Jagged1 levels were increased and decreased in myocardial I/R injury model, respectively, while Dex reversed this effect. Moreover, miR-34b-3p was firstly reported to directly bind and decrease Jagged1 expression, thereby inhibiting Notch signaling pathway. Transfection of agomiR-34b-3p or Jagged1 silencing eliminated Dex's defensive impact on OGD/R-induced cardiomyocytes damage. Dex relieved the myocardial I/R injury of rats via inhibiting miR-34b-3p and further activating Notch signaling pathway.

CONCLUSION

Dex protected myocardium from I/R injury via suppressing miR-34b-3p to activate Jagged1-mediated Notch signaling pathway. Our findings revealed a novel mechanism underlying of Dex on myocardial I/R injury.

Association of exosomal miR-96-5p and miR-146a-5p with the disease severity in dengue virus infection

Exosomes are small extracellular vesicles secreted by cells and have a major role in cell-to-cell signaling. As dengue infection progresses from a mild to a severe form of infection, the exosome's microRNA (miRNA) composition might change, which may contribute to pathogenesis. In this study, a comprehensive analysis of serum exosomal miRNAs was performed and their involvement in dengue virus-induced disease progression in an Indian cohort was assessed. Small RNA-seq showed 50 differentially expressed exosomal miRNAs that were significantly dysregulated during dengue infection. After extensive validation, miR-96-5p was found to be significantly upregulated, whereas miR-146a-5p was significantly downregulated with the progression of disease to severe form. Interestingly, a strong positive correlation was found between the expression levels of miR-96-5p and miR-146a-5p and the platelet levels of the patients. Further, study of miR-146a-5p showed that it regulates the expression of the proteins which are involved in the immune responses. These results suggest that miR-96-5p and miR-146a-5p could be used as diagnostic and prognostic markers for dengue disease progression, in addition to the already available biochemical and pathological parameters.

ALKBH5-induced circular RNA NRIP1 promotes glycolysis in thyroid cancer cells by targeting PKM2

Although circular RNAs (circRNAs) are involved in cell proliferation, differentiation, apoptosis, and invasion, the underlying regulatory mechanisms of circRNAs in thyroid cancer have not been fully elucidated. This article aimed to study the role of circRNA regulated by N6-methyladenosine modification in papillary thyroid cancer (PTC). Quantitative real-time PCR, western blotting, and immunohistochemistry were used to investigate the expressions of circRNA nuclear receptor-interacting protein 1 (circNRIP1) in PTC tissues and adjacent noncancerous thyroid tissues. In vitro and in vivo assays were carried out to assess the effects of circNRIP1 on PTC glycolysis and growth. The N6-methyladenosine mechanisms of circNRIP1 were evaluated by methylated RNA immunoprecipitation sequencing, luciferase reporter gene, and RNA stability assays. Results showed that circNRIP1 levels were significantly upregulated in PTC tissues. Furthermore, elevated circNRIP1 levels in PTC patients were correlated with high tumor lymph node metastasis stage and larger tumor sizes. Functionally, circNRIP1 significantly promoted glycolysis, PTC cell proliferation in vitro, and tumorigenesis in vivo. Mechanistically, circNRIP1 acted as a sponge for microRNA (miR)-541-5p and miR-3064-5p and jointly upregulated pyruvate kinase M2 (PKM2) expression. Knockdown of m⁶ A demethylase α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) significantly enhanced circNRIP1 m⁶ A modification and upregulated its expression. These results show that ALKBH5 knockdown upregulates circNRIP1, thus promoting glycolysis in PTC cells. Therefore, circNRIP1 can be a prognostic biomarker and therapeutic target for PTC by acting as a sponge for oncogenic miR-541-5p and miR-3064-5p to upregulate PKM2 expression.

Circadian system microRNAs - Role in the development of cardiovascular diseases

Circadian rhythm regulates numerous physiological processes, and disruption of the circadian clock can lead to cardiovascular disease. Cardiovascular disease is the leading cause of morbidity and mortality worldwide. Small non-coding RNAs, microRNAs (miRNAs), are involved in regulating gene expression, both those important for the cardiovascular system and key circadian clock genes. Epigenetic mechanisms based on miRNAs are essential for fine-tuning circadian physiology. Indeed, some miRNAs depend on circadian periodicity, others are under the influence of light, and still others are under the influence of core clock genes. Dysregulation of miRNAs involved in circadian rhythm modulation has been associated with inflammatory conditions of the endothelium and atherosclerosis, which can lead to coronary heart disease and myocardial infarction. Epigenetic processes are reversible through their association with environmental factors, enabling innovative preventive and therapeutic strategies for cardiovascular disease. Here, is a review of recent findings on how miRNAs modulate circadian rhythm desynchronization in cardiovascular disease. In the era of personalized medicine, the possibility of treatment with miRNA antagomirs should be time-dependent to correspond to chronotherapy and achieve the most significant efficacy.

Oligo-Not Only for Silencing: Overlooked Potential for Multidirectional Action in Plants

Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of oligos in plants seems to be even easier. The oligo effect could be similar to that induced by endogenous miRNAs. In general, the action of exogenously introduced nucleic acids (Oligo) can be divided into a direct interaction with nucleic acids (genomic DNA, hnRNA, transcript) and an indirect interaction via the induction of processes regulating gene expression (at the transcriptional and translational levels) involving regulatory proteins using endogenous cellular mechanisms. Presumed mechanisms of oligonucleotides' action in plant cells (including differences from animal cells) are described in this review. Basic principles of oligo action in plants that allow bidirectional changes in gene activity and even those that lead to heritable epigenetic changes in gene expression are presented. The effect of oligos is related to the target sequence at which they are directed. This paper also compares different delivery methods and provides a quick guide to using IT tools to help design oligonucleotides.

Identification and profiling of microRNAs during yak's testicular development

BACKGROUND

Normal testicular development is highly crucial for male reproduction and is a precondition for spermatogenesis that is the production of spermatozoa in the testes. MiRNAs have been implicated in several testicular biological processes, including cell proliferation, spermatogenesis, hormone secretion, metabolism and reproductive regulation. In the present study, we used deep sequencing data to study the functions of miRNAs during testicular development and spermatogenesis, by analyzing the expression patterns of small RNAs in 6-, 18- and 30-month-old yak testis tissues.

RESULTS

A total of 737 known and 359 novel miRNAs were obtained from 6-, 18- and 30-month-old yak testes. In all, we obtained 12, 142 and 139 differentially expressed (DE) miRNAs in 30- vs. 18-, 18- vs. 6-, and 30- vs. 6-month-old testes, respectively. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of all DE miRNA target genes revealed BMP2, TGFB2, GDF6, SMAD6, TGFBR2 and other target genes as participants in different biological processes, including TGF-β, GnRH, Wnt, PI3K-Akt, MAPK signaling pathways and several other reproductive pathways. In addition, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) was used to detect the expression of seven randomly selected miRNAs in 6-, 18- and 30-month-old testes, and the results were consistent with the sequencing data.

CONCLUSIONS

The differential expression of miRNAs in yak testes at different development stages was characterized and investigated using deep sequencing technology. We believe that the results will contribute to further understanding the functions of miRNAs in regulating the development of yak testes and improving the reproductive performance of male yaks.

miR-103-3p Regulates the Differentiation and Autophagy of Myoblasts by Targeting MAP4

Skeletal muscle is the most abundant tissue in mammals, and myogenesis and differentiation require a series of regulatory factors such as microRNAs (miRNAs). In this study, we found that miR-103-3p was highly expressed in the skeletal muscle of mice, and the effects of miR-103-3p on skeletal muscle development were explored using myoblast C2C12 cells as a model. The results showed that miR-103-3p could significantly reduce myotube formation and restrain the differentiation of C2C12 cells. Additionally, miR-103-3p obviously prevented the production of autolysosomes and inhibited the autophagy of C2C12 cells. Moreover, bioinformatics prediction and dual-luciferase reporter assays confirmed that miR-103-3p could directly target the microtubule-associated protein 4 (MAP4) gene. The effects of MAP4 on the differentiation and autophagy of myoblasts were then elucidated. MAP4 promoted both the differentiation and autophagy of C2C12 cells, which was contrary to the role of miR-103-3p. Further research revealed that MAP4 colocalized with LC3 in C2C12 cell cytoplasm, and the immunoprecipitation assay showed that MAP4 interacted with autophagy marker LC3 to regulate the autophagy of C2C12 cells. Overall, these results indicated that miR-103-3p regulated the differentiation and autophagy of myoblasts by targeting MAP4. These findings enrich the understanding of the regulatory network of miRNAs involved in the myogenesis of skeletal muscle.

CircRalgapa1 facilitates morphine tolerance via miR-873a-5p/A20 axis in mice

Morphine tolerance (MT) caused by long-term use of morphine is a major medical problem. The underlying molecular mechanisms of morphine tolerance remain unclear. Here, we establish the morphine tolerance model in mice and verify whether a novel circRNA, circRalgapa1 is involved in morphine tolerance and its specific molecular mechanism. We show that the expression of circRalgapa1 in the spinal cord is significantly down-expressed in the spinal cord of morphine-tolerant mice. CircRalgapa1 is mainly located in the neuronal cytoplasm and co-localizes with miR-873a-5p. Mechanically, circRalgapa1 acts as competing endogenous RNAs (ceRNAs) to regulate the inhibitory of miR-873a-5p on A20 (also known as tumor necrosis factor α-induced protein 3, TNFAIP3). Functionally, overexpression of circRalgapa1 by intrathecal injection of adeno-associated virus (AAV- circRalgapa1) attenuated the formation of morphine tolerance and partially reversed the development of morphine tolerance. Moreover, overexpression of miR-873a-5p blocked the effect of AAV-circRalgapa1 on alleviating morphine tolerance in mice. In conclusion, chronic morphine administration-mediated down-regulation of circRalgapa1 in the spinal cord contributes to morphine tolerance via miR-873a-5p/A20 axis in mice. Overexpression of circRalgapa1 may be a promising RNA-based therapy for morphine tolerance.

Studies on the role of non-coding RNAs in controlling the activity of T cells in asthma

Bronchial asthma, commonly known as asthma, is a chronic inflammatory disease characterized by airway inflammation, increased responsiveness and changes in airway structure. T cells, particularly T helper cells, play a crucial role in the disease. Non-coding RNAs, which are RNAs that do not code for proteins, mainly include microRNAs, long non-coding RNAs, and circular RNAs, play a role in regulating various biological processes. Studies have shown that non-coding RNAs have an important role in the activation and transformation of T cells and other biological processes in asthma. The specific mechanisms and clinical applications are worth further examination. This article reviews the recent research on the role of microRNAs, long non-coding RNAs and circular RNAs in T cells in asthma.

Silencing of the circ-Arhgap5 RNA protects neuronal PC12 cells against injury and depends on the miR-29a-3p/Rock1 axis

Circular RNAs (circRNAs) are abundantly expressed in human central nervous system. Here, we explored the role of circ_Arhgap5 in cerebral ischemia/reperfusion (I/R)-induced nerve injury in PC12 cells and its associated mechanism. Cell proliferation ability was assessed by 5-Ethynyl-2'-deoxyuridine (Edu) assay and 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Flow cytometry (FCM) was applied to assess cell apoptotic rate. Cell death was analyzed by lactate dehydrogenase (LDH) assay. Oxygen-glucose deprivation and reoxygenation (OGD/R) up-regulates the expression of circRNA Rho GTPase activating protein 5 (circ_Arhgap5; mmu_circ_0000377) in PC12 cells. OGD/R exposure inhibited the proliferation and induced the apoptosis of PC12 cells, and the silence of circ_Arhgap5 attenuated OGD/R-induced injury in PC12 cells. miR-29a-3p was identified as a target of circ_Arhgap5 in PC12 cells. Circ_Arhgap5 knockdown-mediated protective effects in OGD/R-induced PC12 cells were reversed by the interference of miR-29a-3p. miR-29a-3p interacted with the 3' untranslated region (3'UTR) of Rho-associated coiled-coil-containing protein kinase 1 (Rock1), and circ_Arhgap5 can positively regulate Rock1 expression by sponging miR-29a-3p in PC12 cells. miR-29a-3p overexpression protected PC12 cells against OGD/R-induced damage by down-regulating Rock1. In conclusion, circ_Arhgap5 silencing protected PC12 cells from OGD/R-induced injury through mediating miR-29a-3p/Rock1 axis.

microRNA regulation of skin pigmentation in golden-back mutant of crucian carp from a rice-fish integrated farming system

BACKGROUND

MicroRNAs (miRNAs) are endogenous small non-coding RNAs (21-25 nucleotides) that act as essential components of several biological processes. Golden-back crucian carp (GBCrC, Carassius auratus) is a naturally mutant species of carp that has two distinct body skin color types (golden and greenish-grey), making it an excellent model for research on the genetic basis of pigmentation. Here, we performed small RNA (sRNA) analysis on the two different skin colors via Illumina sequencing.

RESULTS

A total of 679 known miRNAs and 254 novel miRNAs were identified, of which 32 were detected as miRNAs with significant differential expression (DEMs). 23,577 genes were projected to be the targets of 32 DEMs, primarily those involved in melanogenesis, adrenergic signaling in cardiomyocytes, MAPK signaling pathway and wnt signaling pathway by functional enrichment. Furthermore, we built an interaction module of mRNAs, proteins and miRNAs based on 10 up-regulated and 13 down-regulated miRNAs in golden skin. In addition to transcriptional destabilization and translational suppression, we discovered that miRNAs and their target genes were expressed in the same trend at both the transcriptional and translational levels. Finally, we discovered that miR-196d could be indirectly implicated in regulating melanocyte synthesis and motility in the skin by targeting to myh7 (myosin-7) gene through the luciferase reporter assay, antagomir silencing in vivo and qRT-PCR techniques.

CONCLUSIONS

Our study gives a systematic examination of the miRNA profiles expressed in the skin of GBCrC, assisting in the comprehension of the intricate molecular regulation of body color polymorphism and providing insights for C. auratus breeding research.

RNA-Binding Proteins in Bladder Cancer

RNA-binding proteins (RBPs) are key regulators of transcription and translation, with highly dynamic spatio-temporal regulation. They are usually involved in the regulation of RNA splicing, polyadenylation, and mRNA stability and mediate processes such as mRNA localization and translation, thereby affecting the RNA life cycle and causing the production of abnormal protein phenotypes that lead to tumorigenesis and development. Accumulating evidence supports that RBPs play critical roles in vital life processes, such as bladder cancer initiation, progression, metastasis, and drug resistance. Uncovering the regulatory mechanisms of RBPs in bladder cancer is aimed at addressing the occurrence and progression of bladder cancer and finding new therapies for cancer treatment. This article reviews the effects and mechanisms of several RBPs on bladder cancer and summarizes the different types of RBPs involved in the progression of bladder cancer and the potential molecular mechanisms by which they are regulated, with a view to providing information for basic and clinical researchers.

miRNA-Induced Downregulation of IPMK in Macrophages Mediates Lipopolysaccharide-Triggered TLR4 Signaling

Inositol polyphosphate multikinase (IPMK) is a pleiotropic enzyme responsible for the production of inositol polyphosphates and phosphoinositide. IPMK in macrophages was identified as a key factor for the full activation of the Toll-like receptor 4 (TLR4) signaling pathway and inflammation by directly interacting with tumor necrosis factor receptor-associated factor 6 (TRAF6). Here, dynamic changes of IPMK levels in lipopolysaccharide (LPS)-stimulated macrophages and their functional significance were investigated. Both the mRNA and protein levels of IPMK were acutely decreased in mouse and human macrophages when cells were stimulated with LPS for between 1 and 6 h. Analysis of the 3' untranslated region (UTR) of mouse IPMK mRNA revealed a highly conserved binding site for miR-181c. Transfection of miR-181c mimics into RAW 264.7 macrophages led to decreased IPMK 3'UTR-luciferase reporter activity and lowered endogenous IPMK levels. When the genomic deletion of a 33-bp fragment containing a putative miR-181c-binding site was introduced within the IPMK 3'UTR of RAW 264.7 macrophages (264.7^Δ3'UTR), LPS-triggered downregulation of IPMK levels was prevented. LPS treatment in 264.7^Δ3'UTR macrophages decreased TLR4-induced signaling and the expression of proinflammatory cytokines. In response to LPS stimulation, K63-linked ubiquitination of TRAF6 was impaired in 264.7^Δ3'UTR macrophages, suggesting an action of IPMK in the suppression of TRAF6 activation. Therefore, our findings reveal that LPS-mediated suppression of IPMK regulates the full activation of TLR4 signaling and inflammation in macrophages.

MicroRNA biomarkers of type 2 diabetes: evidence synthesis from meta-analyses and pathway modelling

AIMS/HYPOTHESIS

MicroRNAs are being sought as biomarkers for the early identification of type 2 diabetes. This study aimed to synthesise the evidence from microRNA-type 2 diabetes association studies and microRNA-regulated type 2 diabetes pathway delineation studies that met stringent quality criteria to identify and validate microRNAs of both statistical and biological significance as type 2 diabetes biomarkers.

METHODS

Eligible controlled studies on microRNA expression profiling of type 2 diabetes were retrieved from PubMed, ScienceDirect and Web of Science. MicroRNA-regulated type 2 diabetes pathway delineation studies were conducted by integrating and cross-verifying the data from miRTarBase, TransmiR, miRecords, TargetScanHuman, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Retraction Watch database. Before meta-analysis, quality assessment was performed according to the corresponding reporting guidelines for evidence-based medicine. To select the most statistically significant microRNAs, we conducted extensive meta-analyses according to the latest methodology. Subgroup and sensitivity analyses were carried out to further examine the microRNA candidates for their tissue specificity and blood fraction specificity and the robustness of the evidence. Signalling pathway impact analysis of dysregulated microRNAs identified from meta-analyses was performed to select biologically significant microRNAs that were enriched in our newly built microRNA-regulated pathways.

RESULTS

Of the 404 differentially expressed microRNAs identified in the 156 controlled profiling studies with a combined sample size of >15,000, only 60 were both consistently and significantly dysregulated in human type 2 diabetes. No microRNAs were both consistently and significantly dysregulated in multiple tissues according to subgroup analyses. In total, 58 microRNAs were found to be robust in sensitivity analyses. A total of 1966 pathway delineation studies were identified, including 3290 microRNA-target interactions, which were further combined with KEGG pathways, producing 225 microRNA-regulated pathways. Impact analysis found that 16 dysregulated microRNAs identified from extensive meta-analyses were statistically significantly enriched in the augmented KEGG type 2 diabetes pathway.

CONCLUSIONS/INTERPRETATION

Sixteen microRNAs met the criteria for biomarker selection. In terms of both significance and relevance, the order of priority for verification of these microRNAs is as follows: miR-29a-3p, miR-221-3p, miR-126-3p, miR-26a-5p, miR-503-5p, miR-100-5p, miR-101-3p, mIR-103a-3p, miR-122-5p, miR-199a-3p, miR-30b-5p, miR-130a-3p, miR-143-3p, miR-145-5p, miR-19a-3p and miR-311-3p.

REGISTRATION

PROSPERO registration number CRD42017081659.

CircMAP3K4 protects human lens epithelial cells from H2O2-induced dysfunction by targeting miR-193a-3p/PLCD3 axis in age-related cataract

Circular RNAs (circRNAs) have shown pivotal regulatory roles in multiple human ocular diseases, including age-related cataract (ARC). Here, we explored the role of circRNA mitogen-activated protein kinase kinase kinase 4 (circMAP3K4, hsa_circ_0078619) in ARC pathology and its associated mechanism. The expression of RNAs and proteins was examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot assay. Cell viability, senescence, proliferation, and apoptosis were analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, senescence-associated-β-galactosidase (SA-β-Gal) staining, 5-ethynyl-20-deoxyuridine (EdU) assay, and flow cytometry. The oxidative stress status of SRA01/04 cells was analyzed using the commercial kits. The interaction between microRNA-193a-3p (miR-193a-3p) and circMAP3K4 or phospholipase C delta 3 (PLCD3) was verified by dual-luciferase reporter assay, RNA immunoprecipitation (RIP) assay, and RNA-pull down assay. CircMAP3K4 was significantly down-regulated in ARC patients and H2O2-induced SRA01/04 cells. H2O2 treatment restrained the viability and proliferation and promoted the senescence, apoptosis, and oxidative stress of SRA01/04 cells, and circMAP3K4 overexpression protected SRA01/04 cells from H2O2-induced dysfunction. MiR-193a-3p was a direct target of circMAP3K4, and circMAP3K4 overexpression-mediated protective effects in H2O2-induced SRA01/04 cells were largely reversed by the accumulation of miR-193a-3p. MiR-193a-3p interacted with the 3' untranslated region (3'UTR) of PLCD3, and PLCD3 knockdown largely overturned miR-193a-3p silencing-induced protective effects in H2O2-induced SRA01/04 cells. CircMAP3K4 up-regulated the expression of PLCD3 via sponging miR-193a-3p in SRA01/04 cells. In conclusion, circMAP3K4 protected SRA01/04 cells from H2O2-induced dysfunction in ARC through mediating miR-193a-3p/PLCD3 axis.

Dissecting contributions of representative heavy metal components in PM2.5 to its cytotoxicity

PM_2.5 is a complex pollutant that is a pervasive threat to human health. The health risks and toxicity mechanisms of PM_2.5 components must be identified to alleviate the corresponding risks. In this study, a reductionism approach based on model PM_2.5 particles was used to investigate the contributions of the most harmful components in PM_2.5 to its toxicity. Human liver and kidney cells were used as models. The results showed that Cr(VI) was the most critical toxic component among other components (Pb, As, and benzo[a]pyrene) in human liver and kidney cells. PM_2.5-Cr(VI) induced oxidative stress, which led to cytotoxicity by inducing cell cycle arrest in the S-phase in HepG2 and HEK293 cells. The presented findings can provide valuable insights into the toxicity levels of PM_2.5 components, which can help clarify the potential health risks from PM_2.5 exposure.

Functional Relevance of the Long Intergenic Non-Coding RNA Regulator of Reprogramming (Linc-ROR) in Cancer Proliferation, Metastasis, and Drug Resistance

Cancer is responsible for more than 10 million deaths every year. Metastasis and drug resistance lead to a poor survival rate and are a major therapeutic challenge. Substantial evidence demonstrates that an increasing number of long non-coding RNAs are dysregulated in cancer, including the long intergenic non-coding RNA, regulator of reprogramming (linc-ROR), which mostly exerts its role as an onco-lncRNA acting as a competing endogenous RNA that sequesters micro RNAs. Although the properties of linc-ROR in relation to some cancers have been reviewed in the past, active research appends evidence constantly to a better comprehension of the role of linc-ROR in different stages of cancer. Moreover, the molecular details and some recent papers have been omitted or partially reported, thus the importance of this review aimed to contribute to the up-to-date understanding of linc-ROR and its implication in cancer tumorigenesis, progression, metastasis, and chemoresistance. As the involvement of linc-ROR in cancer is elucidated, an improvement in diagnostic and prognostic tools could promote and advance in targeted and specific therapies in precision oncology.

MiR-568 mitigated cardiomyocytes apoptosis, oxidative stress response and cardiac dysfunction via targeting SMURF2 in heart failure rats

Chronic heart failure (CHF), a conventional, complex, and severe syndrome, is generally defined by myocardial output inadequate to satisfy the metabolic requirements of body tissues. Recently, miR-568 was identified to be down-regulated in CHF patients' sera and negatively correlated with left ventricular mass index in symptomatic CHF patients with systolic dysfunction. Nevertheless, the role of miR-568 during CHF development remains obscure. The current study is aimed to investigate the role of miR-568 in CHF. The MTT assay, flow cytometry analysis, RT-qPCR analysis, western blot analysis and luciferase reporter assays were conducted to figure out the function and potential mechanism of miR-568 in vitro. Rats were operated with aortic coarctation to establish CHF animal model. The effects of miR-568 and SMURF2 on CHF rats were evaluated by hematoxylin-eosin staining, Masson's staining, serum index testing, cardiac ultrasound detection, and TUNEL staining assays. We discovered that miR-568 level was downregulated by H₂O₂ treatment in cardiomyocytes. In mechanism, miR-568 directly targeted and negatively regulated SMURF2. In function, SMURF2 overexpression reversed the effects of miR-568 on cardiac function and histological changes in vivo. Additionally, SMURF2 overexpression reversed the effects of miR-568 on the content of LDH, AST, CK and CK-MB in vivo. Moreover, SMURF2 overexpression reversed the effects of miR-568 on oxidative stress response in vivo. MiR-568 mitigated cardiomyocytes apoptosis, oxidative stress response and cardiac dysfunction via targeting SMURF2 in CHF rats. This discovery may serve as a potential biomarker for CHF treatment.

Circ_0006667 contributes to high glucose-induced retinal pigment epithelial cell dysfunction by mediating miR-7-5p/TGFA axis in diabetic retinopathy

BACKGROUND

Diabetic retinopathy (DR) is a common complication of diabetes mellitus and it can lead to visual impairment and blindness. The loss of retinal pigment epithelial (RPE) cells is associated with the etiology of DR. Moreover, dysregulated circular RNAs (circRNAs) are implicated in DR progression. Therefore, this project aims to explore the role and potential mechanism of circ_0006667 in DR.

METHODS

RPE cells (ARPE-19) were stimulated with high glucose (33 mM; HG group) for 24 h to establish the DR cell model. Circ_0006667, microRNA-7-5p (miR-7-5p), and transforming growth factor alpha (TGFA) expression was determined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Cell viability, proliferation, and apoptosis were analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), and flow cytometry. CyclinD1, Cleaved-caspase-3, and TGFA protein levels were detected using western blot. Using Circinteractome and starBase analysis, the binding miR-7-5p and circ_0006667 or TGFA was predicted, and then validated using dual-luciferase reporter and RNA Immunoprecipitation (RIP).

RESULTS

Circ_0006667 expression was up-regulated in DR patients and HG-induced ARPE-19 cells. HG stimulation suppressed ARPE-19 cell proliferation and promoted cell apoptosis and inflammation, which were alleviated via circ_0006667 silence. Circ_0006667 acted as a molecular sponge for miR-7-5p, and circ_0006667 absence-mediated protective effects in HG-induced ARPE-19 cells were largely overturned by the interference of miR-7-5p. miR-7-5p directly targeted TGFA, and miR-7-5p overexpression protected ARPE-19 cells from HG-induced dysfunction largely by down-regulating TGFA. Circ_0006667 can up-regulate the expression of TGFA by sponging miR-7-5p in ARPE-19 cells.

CONCLUSION

Circ_0006667 silencing protected ARPE-19 cells from HG-induced dysfunction by mediating miR-7-5p/TGFA axis.

Using Mechanistic Models and Machine Learning to Design Single-Color Multiplexed Nascent Chain Tracking Experiments

mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Through simulation, we show that with careful application, this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. The proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell signalling applications requiring simultaneous study of multiple mRNAs.

Circ_0110498 facilitates the cisplatin resistance of non-small cell lung cancer by mediating the miR-1287-5p/RBBP4 axis

BACKGROUND

Circular RNAs (circRNAs) play vital roles in non-small cell lung cancer (NSCLC) progression. Our research analyzed the role of circ_0110498 on the cisplatin (DDP) resistance of NSCLC.

METHODS

Cell glycolysis was analyzed by measuring glucose consumption and lactate production. Protein expression was determined by western blot analysis. The expression of circ_0110498, microRNA (miR)-1287-5p and RBBP4 was detected by RT-qPCR assay. Cell counting kit-8, colony formation and transwell assays, together with flow cytometry were conducted to analyze cell DDP resistance, proliferation, metastasis and apoptosis.

RESULTS

Circ_0110498 expression was elevated in DDP-resistant NSCLC tissues and cells. Circ_0110498 silencing not only suppressed the DDP resistance of NSCLC cells by inhibiting cell growth, metastasis and glycolysis, but also enhanced the DDP sensitivity of NSCLC tumors. MiR-1287-5p was sponged by circ_0110498, and its inhibitor also reversed the effect of circ_0110498 silencing on the DDP resistance of NSCLC cells. MiR-1287-5p interacted with RBBP4, and RBBP4 overexpression partly reversed the inhibitory effect of miR-1287-5p on the DDP resistance of NSCLC cells.

CONCLUSION

Circ_0110498 facilitated DDP resistance partly through mediating the miR-1287-5p/RBBP4 signaling in NSCLC.

miR‑151a‑5p promotes the proliferation and metastasis of colorectal carcinoma cells by targeting AGMAT

Colorectal carcinoma (CRC) is one of the most common types of digestive cancer. It has been reported that the ectopic expression of microRNAs (miRs) plays a critical role in the occurrence and progression of CRC. In addition, it has also been suggested that miR‑151a‑5p may serve as a useful biomarker for the early detection and treatment of different types of cancer and particularly CRC. However, the specific effects and underlying mechanisms of miR‑151a‑5p in CRC remain elusive. The results of the current study demonstrated that miR‑151a‑5p was upregulated in CRC cell lines and clinical tissues derived from patients with CRC. Functionally, the results showed that miR‑151a‑5p significantly promoted CRC cell proliferation, migration and invasion. Additionally, dual luciferase reporter assays verified that agmatinase (AGMAT) was a direct target of miR‑151a‑5p and it was positively associated with miR‑151a‑5p expression. Mechanistically, miR‑151a‑5p could enhance the epithelial‑mesenchymal transition of CRC cells. Taken together, the results of the current study revealed a novel molecular mechanism indicating that the miR‑151a‑5p/AGMAT axis could serve a crucial role in the regulation of CRC and could therefore be considered as a potential therapeutic strategy for CRC.

The hitchhikers' guide to RNA sequencing and functional analysis

DNA and RNA sequencing technologies have revolutionized biology and biomedical sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably low costs. RNA sequencing (RNA-Seq) enables transcript identification and quantification, but once sequencing has concluded researchers can be easily overwhelmed with questions such as how to go from raw data to differential expression (DE), pathway analysis and interpretation. Several pipelines and procedures have been developed to this effect. Even though there is no unique way to perform RNA-Seq analysis, it usually follows these steps: 1) raw reads quality check, 2) alignment of reads to a reference genome, 3) aligned reads' summarization according to an annotation file, 4) DE analysis and 5) gene set analysis and/or functional enrichment analysis. Each step requires researchers to make decisions, and the wide variety of options and resulting large volumes of data often lead to interpretation challenges. There also seems to be insufficient guidance on how best to obtain relevant information and derive actionable knowledge from transcription experiments. In this paper, we explain RNA-Seq steps in detail and outline differences and similarities of different popular options, as well as advantages and disadvantages. We also discuss non-coding RNA analysis, multi-omics, meta-transcriptomics and the use of artificial intelligence methods complementing the arsenal of tools available to researchers. Lastly, we perform a complete analysis from raw reads to DE and functional enrichment analysis, visually illustrating how results are not absolute truths and how algorithmic decisions can greatly impact results and interpretation.

Circulating cervical cancer biomarkers potentially useful in medical attention (Review)

Cervical cancer (CC) is a public health problem worldwide, including Mexico. This type of cancer is the fourth most frequent in women worldwide; in Mexico it is the second most common type in women after breast cancer. The diagnosis of CC is based mainly on Pap smears and colposcopy and the identification of molecular tools that serve as a support for these methods is urgent. Regarding this, differential expressions of specific circulating biomolecules has been detected and, based on this, they have been postulated as potential biomarkers for CC diagnosis, prognosis, and/or to identify the response to treatments. Importantly, the combined analysis of these molecules considerably improves their efficacy as biomarkers and their potential use in the medical attention is promising.

Non-invasive diagnosis of endometriosis: Immunologic and genetic markers

Endometriosis, a benign gynecologic and chronic inflammatory disease, is defined by the presence of endometrial tissue outside the uterus characterized mainly by pelvic pain and infertility. Because endometriosis affects approximately 10% of females, it represents a significant socioeconomic burden worldwide having tremendous impact on daily quality of life. Accurate and prompt diagnosis is crucial for the management of this debilitating disorder. Unfortunately, diagnosis is typically delayed to lack of specific symptoms and readily accessible biomarkers. Although histopathologic examination remains the current gold standard, this approach is highly invasive and not applicable for early screening. Recent work has focused on the identification of reliable biomarkers including immunologic, ie, immune cells, antibodies and cytokines, as well as genetic and biochemical markers, ie, microRNAs, lncRNAs, circulating and mitochondrial nucleic acids, along with some hormones, glycoproteins and signaling molecules. Confirmatory research studies are, however, needed to more fully establish these markers in the diagnosis, progression and staging of these endometrial lesions.

Expression Regulation and Trafficking of Aquaporins

Aquaporins (AQPs) mediate the bidirectional water flow driven by an osmotic gradient. Either gating or trafficking allows for rapid and specific AQP regulation in a tissue-dependent manner. The regulatory mechanisms of AQP2 are discussed mainly in this chapter, as the mechanisms controlling the regulation and trafficking of AQP2 have been very well studied. The targeting of AQP2 to the apical plasma membrane of collecting duct principal cells is mainly regulated by the action of arginine vasopressin (AVP) on the type 2 AVP receptor (V2R), which cause increased intracellular cAMP or elevated intracellular calcium levels. Activation of these intracellular signaling pathways results in vesicles bearing AQP2 transport, docking and fusion with the apical membrane, which increase density of AQP2 on the membrane. The removal of AQP2 from the membrane requires dynamic cytoskeletal remodeling. AQP2 is degraded through the ubiquitin proteasome pathway and lysosomal proteolysis pathway. Finally, we review updated findings in transcriptional and epigenetic regulation of AQP2.

Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation

Biological time keeping, or the duration and tempo at which biological processes occur, is a phenomenon that drives dynamic molecular and morphological changes that manifest throughout many facets of life. In some cases, the molecular mechanisms regulating the timing of biological transitions are driven by genetic oscillations, or periodic increases and decreases in expression of genes described collectively as a "molecular clock." In vertebrate animals, molecular clocks play a crucial role in fundamental patterning and cell differentiation processes throughout development. For example, during early vertebrate embryogenesis, the segmentation clock regulates the patterning of the embryonic mesoderm into segmented blocks of tissue called somites, which later give rise to axial skeletal muscle and vertebrae. Segmentation clock oscillations are characterized by rapid cycles of mRNA and protein expression. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short-lived. Faithful, rhythmic, genetic oscillations are sustained by precise regulation at many levels, including post-transcriptional regulation, and such mechanisms are essential for proper vertebrate development. This article is categorized under: RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Regulation.

Transfection and Thermotolerance Methods for Analysis of miR-570 Targeting the HSP Chaperone Network

Heat shock proteins (HSPs) are key stress proteins induced in cells exposed to proteotoxic insult and are critical for thermotolerance. The dynamic network of chaperone interactions, known as the chaperome, contributes significantly to the proteotoxic cell response and the malignant phenotype in cancer. We identified a potent microRNA, miR-570 that could bind the 3'untranslated regions of multiple HSP mRNAs and inhibit HSP synthesis. Here, we will introduce the transfection and thermotolerance methods for analysis of miR-570 targeting the HSP chaperone network.

Circ-ABCC4 contributes to prostate cancer progression and radioresistance by mediating miR-1253/SOX4 cascade

Circular RNAs (circRNAs) exert pivotal functions in many malignancies. However, the roles of circ-ABCC4 in prostate cancer (PCa) radioresistance and progression remain largely unclear. Cell viability, proliferation, apoptosis, invasion, and radioresistance were evaluated by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide, 5-ethynyl-2'-deoxyuridine, flow cytometry, transwell invasion, and colony formation assays. Tumor xenograft experiment was conducted to assess circ-ABCC4 role in xenograft growth in vivo. Dual-luciferase reporter assay was implemented to test the target relation of microRNA-1253 (miR-1253) and circ-ABCC4 or SRY-box transcription factor 4 (SOX4). Circ-ABCC4 enrichment was prominently raised in PCa tissue specimens and cells. Circ-ABCC4 depletion blocked PCa cell viability, proliferation, invasion, and radioresistance and triggered apoptosis. Circ-ABCC4 silencing aggravated irradiation-induced inhibitory effect on xenografts growth. miR-1253 was a downstream molecule of circ-ABCC4, and circ-ABCC4 depletion-mediated anti-cancer impacts in PCa cells were partly counteracted by decreasing miR-1253 abundance. miR-1253 targeted SOX4 mRNA, and miR-1253 blocked PCa cell malignant phenotypes partly by targeting SOX4. Circ-ABCC4 could enhance SOX4 abundance by absorbing miR-1253. Circ-ABCC4 exerted a pro-tumor activity by facilitating PCa cell viability, proliferation, invasion, and radioresistance and suppressing apoptosis.

Primary and Secondary micro-RNA Modulation the Extrinsic Pathway of Apoptosis in Hepatocellular Carcinoma

Abstract-One of the most common malignant liver diseases is hepatocellular carcinoma, which has a high recurrence rate and a low five-year survival rate. It is very heterogeneous both in structure and between patients, which complicates the diagnosis, prognosis and response to treatment. In this regard, an individualized, patient-centered approach becomes important, in which the use of mimetics and hsa-miRNA inhibitors involved in the pathogenesis of the disease may be determinative. From this point of view hsa-miRNAs are of interest, their aberrant expression is associated with poor prognosis for patients and is associated with tumor progression due to dysregulation of programmed cell death (apoptosis). However, the effect of hsa-miRNA on tumor development depends not only on its direct effect on expression of genes, the primary targets, but also on secondary targets mediated by regulatory pathways. While the former are actively studied, the role of secondary targets of these hsa-miRNAs in modulating apoptosis is still unclear. The present work summarizes data on hsa-miRNAs whose primary targets are key genes of the extrinsic pathway of apoptosis. Their aberrant expression is associated with early disease relapse and poor patient outcome. For these hsa-miRNAs, using the software package ANDSystem, we reconstructed the regulation of the expression of secondary targets and analyzed their impact on the activity of the extrinsic pathway of apoptosis. The potential effect of hsa-miRNAs mediated by action on secondary targets is shown to negatively correlate with the number of primary targets. It is also shown that hsa-miR-373, hsa-miR-106b and hsa-miR-96 have the highest priority as markers of hepatocellular carcinoma, whose action on secondary targets enhances their anti-apoptotic effect.

Relationship between the therapeutic potential of various plant-derived bioactive compounds and their related microRNAs in neurological disorders

BACKGROUND

Neurological disorders, such as ischemic stroke, spinal cord injury, neurodegenerative diseases, and glioblastoma often lead to long-term disability and death. MicroRNAs (miRNAs) are small single-stranded non-coding RNAs of approximately 22 nucleotides, known to participate in both normal and pathological development, making them ideal therapeutic targets for clinical intervention. Several recent studies have suggested that plant-derived bioactive compounds (PDBCs) can have anti-atherosclerosis, antioxidant, and anti-inflammatory effects by regulating miRNAs. Thus, miRNAs are novel targets for the action of PDBCs.

PURPOSE

The aim of this review was to evaluate the current status of PDBCs targeted miRNAs by dissecting their development status through a literature review.

METHODS

A manual and electronic search was performed for English articles available from inception up to June 2022 reporting PDBCs and their regulating relationship with miRNAs for the therapeutic potential of neurological disorders. Information was retrieved from scientific databases including PubMed, ScienceDirect, Web of Science, Google Scholar and Chemical Abstracts Services. Keywords used for the search engines were "miRNAs" AND "Plant-derived bioactive compounds" in conjunction with "(native weeds OR alien invasive)" AND "traditional herbal medicine".

RESULTS

A total of 37 articles were retrieved on PDBCs and their related miRNAs in neurological disorders. These PDBCs from traditional herbal medicine may play a therapeutic role in neurological disorders in a variety of mechanisms by regulating the corresponding miRNAs. These mechanisms mainly include inhibiting oxidative stress, anti-neuroinflammation, anti-autophagy, and anti-apoptosis. PDBC are a group of chemically distinct compounds derived from medicinal plants, some of which have therapeutic effects on neurological disorders.

CONCLUSION

The emergence of miRNAs as pathological regulatory factors provides a new direction for the study of bioactive compounds in Traditional Chinese medicine and the elucidating of their epigenetic effects. Elucidating the regulatory relationship between bioactive compounds and miRNAs may help to identify new therapeutic targets and promoting the application of these compounds in precision medicine through their targeted molecular activity.

Circ_0138960 knockdown alleviates lipopolysaccharide-induced inflammatory response and injury in human dental pulp cells by targeting miR-545-5p/MYD88 axis in pulpitis

Background/purpose

Circular RNAs (circRNAs) have been shown to play important regulatory roles in many human diseases, yet their functions in pulpitis remain to be clarified. This study was designed to investigate the function of circ_0138960 in pulpitis progression and its underlying mechanism.

Material and methods

Cell viability and proliferation were analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and 5-Ethynyl-2'-deoxyuridine (EdU) assay. Flow cytometry and enzyme-linked immunosorbent assay (ELISA) were conducted to analyze cell apoptosis rate and the release of inflammatory cytokines. The activity of superoxide dismutase (SOD) was analyzed using a SOD assay kit. Dual-luciferase reporter and RNA-pull down assays were performed to verify the interaction between microRNA-545-5p (miR-545-5p) and circ_0138960 or myeloid differentiation primary response gene 88 (MYD88).

Results

Lipopolysaccharide (LPS) treatment restrained the proliferation and promoted the apoptosis, inflammation, and oxidative stress of human dental pulp cells (hDPCs). LPS treatment dose-dependently up-regulated circ_0138960 expression in hDPCs. Circ_0138960 knockdown overturned LPS-induced inflammation and injury in hDPCs. Circ_0138960 could act as a molecular sponge for miR-545-5p, and circ_0138960 knockdown protected hDPCs from LPS-induced effects by up-regulating miR-545-5p. miR-545-5p directly interacted with the 3' untranslated region (3'UTR) of MYD88, and MYD88 overexpression reversed miR-545-5p-mediated effects in LPS-treated hDPCs. Circ_0138960 positively regulated MYD88 expression by sponging miR-545-5p in hDPCs. LPS could activate nuclear factor kappa-B (NF-κB) signaling by targeting circ_0138960/miR-545-5p/MYD88 axis in hDPCs.

Conclusion

Circ_0138960 knockdown attenuated LPS-induced inflammatory response and injury in hDPCs by targeting the miR-545-5p/MYD88/NF-κB axis.

Role of Transcription Factor Nrf2 in Pyroptosis in Spinal Cord Injury by Regulating GSDMD

Spinal cord injury (SCI) is a prevalent disease that debilitates millions of people. Nuclear factor E2-related factor 2 (Nrf2) is an important regulator of SCI. The current study sought to elaborate on the effects of Nrf2 on gasdermin D (GSDMD)-mediated microglia pyroptosis to repair SCI. The SCI rat model was established via the percussion of the T10 spinal cord and in vitro SCI model was established on BV-2 cells via lipopolysaccharide (LPS)/adenosine triphosphate (ATP) treatment. Nrf2 expression in SCI rats and BV-2 cells was overexpressed via pcDNA3.1-Nrf2 injection. Functional assays were carried out to evaluate SCI rat pathological injury, BV-2 cell viability, the release of lactate dehydrogenase (LDH), and pyroptotic factors. The binding relations of Nrf2 and microRNA (miR)-146a and miR-146a and GSDMD were verified. BV-2 pyroptosis was analyzed after the combined experiment of miR-146a-inhibitor and pcDNA3.1-GSDMD. Our experiments revealed that Nrf2 was downregulated in SCI, and Nrf2 overexpression relieved SCI pathological injury, promoted BV-2 cell viability, inhibited the release of LDH, and repressed pyroptosis. Mechanically, Nrf2 bound to the miR-146a promoter and promoted miR-146a expression, and miR-146a targeted GSDMD transcription. Rescue experiments revealed that miR-146a knockdown or GSDMD overexpression annulled the inhibitory function of Nrf2 overexpression in LPS/ATP-induced microglia pyroptosis. Overall, our findings initially highlighted that Nrf2 inhibited GSDMD-mediated microglia pyroptosis and accelerated SCI repair by repressing miR-146a.

microRNA-dependent regulation of gene expression in GABAergic interneurons

Information processing within neuronal circuits relies on their proper development and a balanced interplay between principal and local inhibitory interneurons within those circuits. Gamma-aminobutyric acid (GABA)ergic inhibitory interneurons are a remarkably heterogeneous population, comprising subclasses based on their morphological, electrophysiological, and molecular features, with differential connectivity and activity patterns. microRNA (miRNA)-dependent post-transcriptional control of gene expression represents an important regulatory mechanism for neuronal development and plasticity. miRNAs are a large group of small non-coding RNAs (21-24 nucleotides) acting as negative regulators of mRNA translation and stability. However, while miRNA-dependent gene regulation in principal neurons has been described heretofore in several studies, an understanding of the role of miRNAs in inhibitory interneurons is only beginning to emerge. Recent research demonstrated that miRNAs are differentially expressed in interneuron subclasses, are vitally important for migration, maturation, and survival of interneurons during embryonic development and are crucial for cognitive function and memory formation. In this review, we discuss recent progress in understanding miRNA-dependent regulation of gene expression in interneuron development and function. We aim to shed light onto mechanisms by which miRNAs in GABAergic interneurons contribute to sculpting neuronal circuits, and how their dysregulation may underlie the emergence of numerous neurodevelopmental and neuropsychiatric disorders.

Dynamic RNA synthetic biology: new principles, practices and potential

An increased appreciation of the role of RNA dynamics in governing RNA function is ushering in a new wave of dynamic RNA synthetic biology. Here, we review recent advances in engineering dynamic RNA systems across the molecular, circuit and cellular scales for important societal-scale applications in environmental and human health, and bioproduction. For each scale, we introduce the core concepts of dynamic RNA folding and function at that scale, and then discuss technologies incorporating these concepts, covering new approaches to engineering riboswitches, ribozymes, RNA origami, RNA strand displacement circuits, biomaterials, biomolecular condensates, extracellular vesicles and synthetic cells. Considering the dynamic nature of RNA within the engineering design process promises to spark the next wave of innovation that will expand the scope and impact of RNA biotechnologies.

Bioinformatics analysis of the common targets of miR-223-3p, miR-122-5p, and miR-93-5p in polycystic ovarian syndrome

Polycystic ovarian syndrome (PCOS) is one of the most common gynecological endocrine disorders. MicroRNAs (miRNAs) play extensive roles in the pathogenesis of PCOS and can serve as potential diagnostic markers. However, most studies focused on the regulatory mechanisms of individual miRNAs, and the combined regulatory effects of multiple miRNAs remain unclear. The aim of this study was to identify the common targets of miR-223-3p, miR-122-5p, and miR-93-5p; and assess the transcript levels of some of these targets in PCOS rat ovaries. Transcriptome profiles of granulosa cells from PCOS patients were obtained from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs). A total of 1,144 DEGs were screened, 204 of which were upregulated and 940 were downregulated. According to the miRWalk algorithm, 4,284 genes were targeted by all three miRNAs at the same time, and intersection with DEGs was used to obtain candidate target genes. A total of 265 candidate target genes were screened, and the detected target genes were subjected to Gene ontology (GO) and KEGG pathway enrichment, followed by PPI network analysis. Then, qRT-PCR was used to determine the levels of 12 genes in PCOS rat ovaries. The expressions of 10 of these genes were found to be consistent with our bioinformatics results. In conclusion, JMJD1C, PLCG2, SMAD3, FOSL2, TGFB1, TRIB1, GAS7, TRIM25, NFYA, and CALCRL may participate in the development of PCOS. Our findings contribute to the identification of biomarkers that may promote the effective prevention and treatment of PCOS in the future.

LOC554202 contributes to chordoma progression by sponging miR-377-3p and up-regulating SMAD3

Chordoma is a rare malignant bone tumor originating from the remnants of the notochord. Here, the role of long noncoding LOC554202 in chordoma progression and its associated mechanism were explored. Cell proliferation was analyzed by 3-(4, 5-dimethylthiazol-2-yl)-2, 5 diphenyltetrazolium bromide and colony formation assays. Flow cytometry was conducted to analyze cell apoptosis rate. The migration and invasion of chordoma cells were analyzed by transwell migration and invasion assays and wound healing assays. A xenograft tumor model was established in nude mice to explore the role of LOC554202 in regulating tumor growth in vivo . The interaction between microRNA-377-3p (miR-377-3p) and LOC554202 or sekelsky mothers against d PP (SMAD) family member 3 (SMAD3) was verified by dual-luciferase reporter and RNA immunoprecipitation assays. The glycolytic rate of chordoma cells was analyzed using glucose assay kit, lactic acid kit and ApoSENSOR ADP/ATP ratio assay kit. LOC554202 expression was upregulated in chordoma tissues and cell lines. LOC554202 silencing suppressed the proliferation, migration and invasion and induced the apoptosis of chordoma cells. LOC554202 knockdown restrained xenograft tumor growth in vivo . miR-377-3p was confirmed as a target of LOC554202, and miR-377-3p silencing largely overturned LOC554202 knockdown-mediated anti-tumor effects in chordoma cells. miR-377-3p interacted with the 3' untranslated region (3'UTR) of SMAD3 and miR-377-3p overexpression-mediated antitumor effects in chordoma cells were largely attenuated by SMAD3 overexpression. LOC554202 could positively regulate SMAD3 expression by sponging miR-377-3p in chordoma cells. LOC554202 contributed to the glycolysis of chordoma cells by targeting binding to miR-377-3p/SMAD3 axis. LOC554202 facilitated the proliferation, migration, invasion and glycolysis and inhibited the apoptosis of chordoma cells by mediating miR-377-3p/SMAD3 axis.

NF-κB1 p50 stabilizes HIF-1α protein through suppression of ATG7-dependent autophagy

The function and underlying mechanisms of p50 in the regulation of protein expression is much less studied because of its lacking of transactivation domain. In this study, we discovered a novel function of p50 in its stabilization of hypoxia-inducible factor 1α (HIF-1α) protein under the condition of cells exposed to arsenic exposure. In p50-deficient (p50^-/-) cells, the HIF-1α protein expression was impaired upon arsenic exposure, and such defect could be rescued by reconstitutional expression of p50. Mechanistic study revealed that the inhibition of autophagy-related gene 7 (ATG7)-dependent autophagy was in charge of p50-mediated HIF-1α protein stabilization following arsenic exposure. Moreover, p50 deletion promoted nucleolin (NCL) protein translation to enhance ATG7 mRNA transcription via directly binding transcription factor Sp1 mRNA and increase its stability. We further discovered that p50-mediated miR-494 upregulation gave rise to the inhibition of p50-mediated NCL translation by interacting with its 3'-UTR. These novel findings provide a great insight into the understanding of biomedical significance of p50 protein in arsenite-associated disease development and therapy.

Tumor Cell-Derived Exosomal circ-PRKCI Promotes Proliferation of Renal Cell Carcinoma via Regulating miR-545-3p/CCND1 Axis

Renal cell carcinoma (RCC) originates from the epithelial cells of the renal tubules and has a high degree of malignancy and heterogeneity. Recent studies have found that exosomes regulate intercellular communication via transferring various bioactive molecules, such as circular RNAs (circRNAs), which are critical for cancer progression. However, the role of tumor cell-derived exosomal circRNAs in RCC remains unclear. In this study, we reported the high expression of circ-PRKCI in RCC tissues and serum exosomes. We also found that circ-PRKCI could be transferred exosomally from highly malignant RCC cells to relatively less malignant RCC cells. Tumor cell-derived exosomal circ-PRKCI promoted the proliferation, migration, and invasion of RCC cells, while inhibiting their apoptosis. Mechanistically, we found that circ-PRKCI promoted the proliferation of RCC via the miR-545-3p/CCND1 signaling pathway. Our study is the first to report the potential mechanisms of tumor cell-derived exosomal circ-PRKCI in RCC. In conclusion, this study will provide a new understanding about the molecular mechanisms of RCC progression.

Selective extracellular secretion of small double-stranded RNA by Tetragenococcus halophilus

Small double-stranded RNAs (dsRNAs) abundantly produced by lactic acid bacteria demonstrate immunomodulatory activity and antiviral protective immunity. However, the extracellular secretion of dsRNA from lactic acid bacteria and their compositional and functional differences compared to the intracellular dsRNA is unknown. In this study, we compared the intracellular and secreted extracellular dsRNA of the lactic acid bacteria, Tetragenococcus halophilus, commonly present in fermented foods, by growing in RNA-free and RNase-free media. We used RNA deep sequencing and in-silico analysis to annotate potential regulatory functions for the comparison. A time series sampling of T. halophilus culture demonstrated growth phase-dependent dynamics in extracellular dsRNA secretion with no major change in the intracellular dsRNA profile. The RNA deep sequencing resulted in thousands of diverse dsRNA fragments with 14-21 nucleotides in size from T. halophilus culture. Over 70% of the secreted extracellular dsRNAs were unique in their sequences compared to the intracellular dsRNAs. Furthermore, the extracellular dsRNA abundantly contains sequences that are not T. halophilus genome encoded, not detected intracellularly and showed higher hits on human transcriptome during in-silico analysis, which suggests the presence of extrachromosomal mobile regulatory elements. Further analysis showed significant enrichment of dsRNA target genes of human transcriptome on cancer pathways and transcription process, indicating the extracellular dsRNA of T. halophilus is different not only at the sequence level but also in function. Studying the bacterial extracellular dsRNA is a promising area of future research, particularly for developing postbiotic fermented functional foods and understanding the impact of commensal gut bacteria on human health.

Analysis of aberrant miRNA-mRNA interaction networks in prostate cancer to conjecture its molecular mechanisms

BACKGROUND

MicroRNAs (miRNAs) capable of post-transcriptionally regulating mRNA expression are essential to tumor occurrence and progression.

OBJECTIVE

This study aims to find negatively regulatory miRNA-mRNA pairs in prostate adenocarcinoma (PRAD).

METHODS

Combining The Cancer Genome Atlas (TCGA) RNA-Seq data with Gene Expression Omnibus (GEO) mRNA/miRNA expression profiles, differently expressed miRNA/mRNA (DE-miRNAs/DE-mRNAs) were identified. MiRNA-mRNA pairs were screened by miRTarBase and TarBase, databases collecting experimentally confirmed miRNA-mRNA pairs, and verified in 30 paired prostate specimens by real-time reverse transcription polymerase chain reaction (RT-qPCR). The diagnostic values of miRNA-mRNA pairs were measured by receiver operation characteristic (ROC) curve and Decision Curve Analysis (DCA). DAVID-mirPath database and Connectivity Map were employed in GO/KEGG analysis and compounds research. Interactions between miRNA-mRNA pairs and phenotypic features were analyzed with correlation heatmap in hiplot.

RESULTS

Based on TCGA RNA-Seq data, 22 miRNA and 14 mRNA GEO datasets, 67 (20 down and 47 up) miRNAs and 351 (139 up and 212 down) mRNAs were selected. After screening from 2 databases, 8 miRNA (up)-mRNA (down) and 7 miRNA (down)-mRNA (up) pairs were identified with Pearson's correlation in TCGA. By external validation, miR-221-3p (down)/GALNT3 (up) and miR-20a-5p (up)/FRMD6 (down) were chosen. The model combing 4 signatures possessed better diagnostic value. These two miRNA-mRNA pairs were significantly connected with immune cells fraction and tumor immune microenvironment.

CONCLUSIONS

The diagnostic model containing 2 negatively regulatory miRNA-mRNA pairs was established to distinguish PRADs from normal controls.

A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing

BACKGROUND

Posttranscriptional processing of precursor mRNAs contributes to transcriptome and protein diversity and gene regulatory mechanisms in eukaryotes. However, this posttranscriptional mechanism has not been studied in the marine macroalgae Gracilariopsis lemaneiformis, which is the most cultivated red seaweed species in China.

RESULTS

In the present study, third-generation sequencing (Pacific Biosciences single-molecule real-time long-read sequencing, SMRT-Seq) was used to sequence the full-length transcriptome of G. lemaneiformis to identify alternatively spliced transcripts and alternative polyadenylation (APA) sites in this species. RNAs were isolated from G. lemaneiformis under various treatments including abiotic stresses and exogenous phytohormones, and then equally pooled for SMRT-Seq. In summary, 346,544 full-length nonchimeric reads were generated, from which 13,630 unique full-length transcripts were obtained in G. lemaneiformis. Compared with the known splicing events in the gene models, more than 3000 new alternative splicing (AS) events were identified in the SMRT-Seq reads. Additionally, 810 genes were found to have poly (A) sites and 91 microRNAs (miRNAs), 961 long noncoding RNAs and 1721 novel genes were identified in G. lemaneiformis. Moreover, validation experiments showed that abiotic stresses and phytohormones could induce some specific AS events, especially intron retain isoforms, cause some alterations to the relative ratios of transcripts annotated to the same gene, and generate novel 3' ends because of differential APA. The growth of G. lemaneiformis was inhibited by Cu stress, while this inhibition was alleviated by ACC treatment. RNA-Seq analysis further revealed that 211 differential alternative splicing (DAS) events and 142 DAS events was obtained in CK vs Cu and Cu vs Cu + ACC, respectively, suggesting that AS of functional genes could be regulated by Cu stress and ACC. Compared with Cu stress, the expression of transcripts with DAS events mainly involved in the carbon fixation in photosynthetic organisms and oxidative phosphorylation pathway was upregulated in Cu + ACC treatment, revealing that ACC alleviated the growth inhibition by Cu stress by increasing carbon fixation and oxidative phosphorylation.

CONCLUSIONS

Our results provide the first comprehensive picture of the full-length transcriptome and posttranscriptional mechanism in red macroalgae, including transcripts that appeared in the presence of common abiotic stresses and phytohormones, which will improve the gene annotations of Gracilariopsis and contribute to the study of gene regulation in this important cultivated seaweed.

Challenging Cellular Homeostasis: Spatial and Temporal Regulation of miRNAs

Mature microRNAs (miRNAs) are single-stranded non-coding RNA (ncRNA) molecules that act in post-transcriptional regulation in animals and plants. A mature miRNA is the end product of consecutive, highly regulated processing steps of the primary miRNA transcript. Following base-paring of the mature miRNA with its mRNA target, translation is inhibited, and the targeted mRNA is degraded. There are hundreds of miRNAs in each cell that work together to regulate cellular key processes, including development, differentiation, cell cycle, apoptosis, inflammation, viral infection, and more. In this review, we present an overlooked layer of cellular regulation that addresses cell dynamics affecting miRNA accessibility. We discuss the regulation of miRNA local storage and translocation among cell compartments. The local amounts of the miRNAs and their targets dictate their actual availability, which determines the ability to fine-tune cell responses to abrupt or chronic changes. We emphasize that changes in miRNA storage and compactization occur under induced stress and changing conditions. Furthermore, we demonstrate shared principles on cell physiology, governed by miRNA under oxidative stress, tumorigenesis, viral infection, or synaptic plasticity. The evidence presented in this review article highlights the importance of spatial and temporal miRNA regulation for cell physiology. We argue that limiting the research to mature miRNAs within the cytosol undermines our understanding of the efficacy of miRNAs to regulate cell fate under stress conditions.