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Methods in Enzymology 2023MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a crucial role in gene silencing. The gene-silencing activity of miRNAs depends on their sequences and...
MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a crucial role in gene silencing. The gene-silencing activity of miRNAs depends on their sequences and expression levels. The human RNase III enzyme DICER cleaves miRNA precursors (pre-miRNAs) to produce miRNAs, making it crucial for miRNA production and cellular miRNA functions. DICER is also critical for the gene silencing technology using short-hairpin RNAs (shRNAs), which are cleaved by DICER to generate siRNAs that knockdown target genes. The DICER cleavage assay is an important tool for investigating its molecular mechanisms, which are essential for understanding its functions in miRNA biogenesis and shRNA-based gene silencing technology. The assay involves DICER protein purification, preparation of pre-miRNA and shRNA substrates, and the cleavage assay, using common molecular biology equipment and commercialized reagents that can be applied to other RNA endonucleases.
Topics: Humans; MicroRNAs; Ribonuclease III; RNA, Small Interfering; RNA, Double-Stranded
PubMed: 37925182
DOI: 10.1016/bs.mie.2023.02.023 -
Human Reproduction (Oxford, England) Dec 2023Endometriosis is defined by the presence of extrauterine endometrial-like tissue, which can cause pain and infertility in 10% of reproductive-age women. To date, the... (Review)
Review
Endometriosis is defined by the presence of extrauterine endometrial-like tissue, which can cause pain and infertility in 10% of reproductive-age women. To date, the pathogenesis is poorly understood resulting in significant diagnostic delays and poor therapeutic outcomes in many women. Small extracellular vesicles (sEVs) (<200 nm) are cell-derived vesicles containing molecules that can influence gene expression and behaviour in target cells. One such cargo are microRNAs (miRNAs), which are short, non-coding RNAs mostly 19-25 nucleotides in length that regulate post-transcriptional gene expression. This mini-review focuses on the role of sEV-miRNAs, which are conceivably better biomarkers for endometriosis than free miRNAs, which reflect the true pathophysiological state in the body, as sEV-encapsulated miRNAs are protected from degradation compared to free miRNA and provide direct cell-to-cell communication via sEV surface proteins. sEV-miRNAs have been implicated in the immunomodulation of macrophages, the proliferation, migration and invasion of endometrial cells, and angiogenesis, all hallmarks of endometriosis. The diagnostic potential of sEV-miRNA was investigated in one study that reported the sensitivity and specificity of two sEV-miRNAs (hsa-miR-22-3p and hsa-miR-320a-3p) in distinguishing endometriosis from non-endometriosis cases. Only three studies have explored the therapeutic potential of sEV-miRNAs in vivo in mice-two looked into the role of sEV-hsa-miR-214-3p in decreasing fibrosis, and one investigated sEV-hsa-miR-30c-5p in suppressing the invasive and migratory potential of endometriotic lesions. While early results are encouraging, studies need to further address the potential influence of factors such as the menstrual cycle as well as the location and extent of endometriotic lesions on miRNA expression in sEVs. Given these findings, and extrapolating from other conditions such as cancer, diabetes, and pre-eclampsia, sEV-miRNAs could present an attractive and urgently needed future diagnostic and therapeutic target for millions of women suffering from endometriosis. However, research in this area is hampered by lack of adherence to the International Society for Extracellular Vesicles 2018 guideline in separating and characterising sEVs, as well as the World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project protocols.
Topics: Humans; Female; Animals; Mice; Endometriosis; Biological Specimen Banks; MicroRNAs; Extracellular Vesicles; Biomarkers
PubMed: 37877421
DOI: 10.1093/humrep/dead216 -
Annals of Medicine Dec 2022MicroRNAs (miRNAs) are a class of small non-coding, single-stranded RNAs (ribonucleic acids) that play important roles in many vital processes through their impact on... (Review)
Review
MicroRNAs (miRNAs) are a class of small non-coding, single-stranded RNAs (ribonucleic acids) that play important roles in many vital processes through their impact on gene expression. One such miRNA, miR210, represents a hypoxia-induced cellular miRNA group that hold a variety of functions. This review article highlights the importance of miR-210 in the development of pre-eclampsia.KEY MESSAGEmiR-210 is a promising biomarker for monitoring pregnancy with pre-eclampsia. Overexpression of miR-210 had a negative impact on the process of cell migration and trophoblast invasion.
Topics: Cell Movement; Female; Humans; MicroRNAs; Placenta; Pre-Eclampsia; Pregnancy; Trophoblasts
PubMed: 35543206
DOI: 10.1080/07853890.2022.2071459 -
RNA (New York, N.Y.) Jul 2022Hairpin-containing pre-miRNAs, produced from pri-miRNAs, are precursors of miRNAs (microRNAs) that play essential roles in gene expression and various human diseases....
Hairpin-containing pre-miRNAs, produced from pri-miRNAs, are precursors of miRNAs (microRNAs) that play essential roles in gene expression and various human diseases. Current qPCR-based methods used to quantify pre-miRNAs are not effective to discriminate between pre-miRNAs and their parental pri-miRNAs. Here, we developed the intramolecular ligation method (iLIME) to quantify and sequence pre-miRNAs specifically. This method utilizes T4 RNA ligase 1 to convert pre-miRNAs into circularized RNAs, allowing us to design PCR primers to quantify pre-miRNAs, but not their parental pri-miRNAs. In addition, the iLIME also enables us to sequence the ends of pre-miRNAs using next-generation sequencing. Therefore, this method offers a simple and effective way to quantify and sequence pre-miRNAs, so it will be highly beneficial for investigating pre-miRNAs when addressing research questions and medical applications.
Topics: High-Throughput Nucleotide Sequencing; Humans; MicroRNAs; Real-Time Polymerase Chain Reaction
PubMed: 35487691
DOI: 10.1261/rna.079101.122 -
International Journal of Molecular... Sep 2022Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown... (Review)
Review
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules.
Topics: Animals; Gene Expression Regulation, Plant; MicroRNAs; Plants, Medicinal; RNA, Messenger; RNA, Plant; RNA, Ribosomal
PubMed: 36142389
DOI: 10.3390/ijms231810477 -
Psychoneuroendocrinology Nov 2020Depression is one of the most prevalent, disabling, and costly mental illnesses currently affecting over 300 million people worldwide. A subset of depressed patients... (Review)
Review
Depression is one of the most prevalent, disabling, and costly mental illnesses currently affecting over 300 million people worldwide. A subset of depressed patients display inflammation as indicated by increased levels of proinflammatory mediators in the blood and cerebrospinal fluid. Longitudinal and experimental studies suggest that this inflammatory profile may causally contribute to the initiation, maintenance, or recurrence of depressive episodes in the context of major depressive disorder (MDD). While the mechanistic pathways that mediate these depressogenic effects have not yet been fully elucidated, toll-like receptor (TLR) signaling is one potential common inflammatory pathway. In this review, we focus on the role that inflammation plays in depression, TLR signaling and its plasticity as a candidate pathway, its regulation by micro ribonucleic acids (miRNAs), and their potential as diagnostic biomarkers for identification of inflammatory subtypes of depression. Pre-clinical and clinical studies have demonstrated that TLR expression and TLR signaling regulators are associated with MDD. Further, TLR expression and signaling is in-turn, regulated in part by miRNAs and some TLR-responsive miRNAs indirectly modulate pathways that are implicated in MDD pathophysiology. These data suggest an intersection between TLR signaling regulation and MDD-linked pathways. While these studies suggest that miRNAs play a role in the pathophysiology of MDD via their regulatory effects on TLR pathways, the utility of miRNAs as biomarkers and potential treatment targets remains to be determined. Developing new and innovative techniques or adapting established immunological approaches to mental health, should be at the forefront in moving the field forward, especially in terms of categorization of inflammatory subtypes in MDD.
Topics: Biomarkers; Depression; Depressive Disorder, Major; Humans; Inflammation; MicroRNAs; Signal Transduction; Toll-Like Receptors
PubMed: 32911436
DOI: 10.1016/j.psyneuen.2020.104843 -
International Journal of Biological... Dec 2023The typical function of Drosha is participating in cleaving pri-miRNA, the initial step of miRNA biogenesis, in the nucleus. Since Drosha has a double-stranded... (Review)
Review
The typical function of Drosha is participating in cleaving pri-miRNA, the initial step of miRNA biogenesis, in the nucleus. Since Drosha has a double-stranded RNA-binding domain and two RNase III domains, when it binds and/or cleaves other RNA species other than pri-miRNA, Drosha is able to induce a variety of novel biological effects. Moreover, by interacting with other protein, Drosha is able to modify the function of other protein complexes. Recently, diverse non-classical functions of Drosha have been demonstrated, such as promoting DNA damage repair, transcriptional activation and inhibition, pre-mRNA splicing regulation, mRNA destabilization, and virus-host interaction. In this review, we describe these newly discovered functions of Drosha in order to present a panoramic picture of the novel biological processes that Drosha is involved in.
Topics: Ribonuclease III; MicroRNAs; Proteins; Gene Expression Regulation; RNA Processing, Post-Transcriptional
PubMed: 37793530
DOI: 10.1016/j.ijbiomac.2023.127202 -
Bone Feb 2021During the past several years, pre-clinical experiments have established that microRNAs (miRNAs), small non-coding RNAs, serve as key regulatory molecules of fracture... (Review)
Review
During the past several years, pre-clinical experiments have established that microRNAs (miRNAs), small non-coding RNAs, serve as key regulatory molecules of fracture healing. Their easy modulation with agonists and antagonists make them highly desirable targets for future therapeutic strategies, especially for pathophysiologic fractures that either do not heal (nonunions) or are delayed. It is now well documented that these problematic fractures lead to human suffering and impairment of life quality. Additionally, financial difficulties are also encountered as work productivity decreases and income is reduced. Moreover, targeting miRNAs may also be an avenue to enhancing normal physiological fracture healing. Herein we present the most current knowledge of the involvement of miRNAs during fracture healing in pre-clinical studies. Following a brief description on the nature of miRNAs and of the fracture healing process, we present data from studies focusing specifically, on miRNA regulation of osteoblast differentiation and osteogenesis (within the context of known signaling pathways), chondrocytes, angiogenesis, and apoptosis, all critical to successful bone repair. Further, we also discuss miRNAs and exosomes. We hope that this manuscript serves as a comprehensive review that will facilitate basic/translational scientists in the orthopaedic arena to realize and further decipher the biological and future therapeutic impact of these small regulatory RNA molecules, especially as they relate to the molecular events of each of the major phases of fracture healing.
Topics: Cell Differentiation; Fracture Healing; Fractures, Bone; Humans; MicroRNAs; Osteogenesis
PubMed: 33212318
DOI: 10.1016/j.bone.2020.115758 -
Methods in Molecular Biology (Clifton,... 2022Mature microRNAs (miRNAs) are short RNA sequences about 18-24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of...
Mature microRNAs (miRNAs) are short RNA sequences about 18-24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of target RNAs. Considering the canonical pathway, mature miRNAs are produced via a multistep process. Their transcription (pri-miRNAs) and first processing step via the microprocessor complex (pre-miRNAs) occur in the nucleus. Then they are exported into the cytosol, processed again by Dicer (dsRNA) and finally a single strand (mature miRNA) is incorporated into RISC (miRISC). The sequence of the incorporated miRNA provides the function of RNA target recognition via hybridization. Following binding of the target, the mRNA is either degraded or translation is inhibited, which ultimately leads to less protein production. Conversely, it has been shown that binding within the 5' UTR of the mRNA can lead to an increase in protein product. Regulation of homeostasis is very important for a cell; therefore, all steps in the miRNA-based regulation pathway, from transcription to the incorporation of the mature miRNA into RISC, are under tight control. While much research effort has been exerted in this area, the knowledgebase is not sufficient for accurately modelling miRNA regulation computationally. The computational prediction of miRNAs is, however, necessary because it is not feasible to investigate all possible pairs of a miRNA and its target, let alone miRNAs and their targets. We here point out open challenges important for computational modelling or for our general understanding of miRNA-based regulation and show how their investigation is beneficial. It is our hope that this collection of challenges will lead to their resolution in the near future.
Topics: Gene Expression Regulation; Genomics; MicroRNAs; RNA, Messenger
PubMed: 34432289
DOI: 10.1007/978-1-0716-1170-8_19 -
Science (New York, N.Y.) Mar 2023Mutations in the 3' to 5' RNA exonuclease USB1 cause hematopoietic failure in poikiloderma with neutropenia (PN). Although USB1 is known to regulate U6 small nuclear RNA...
Mutations in the 3' to 5' RNA exonuclease USB1 cause hematopoietic failure in poikiloderma with neutropenia (PN). Although USB1 is known to regulate U6 small nuclear RNA maturation, the molecular mechanism underlying PN remains undetermined, as pre-mRNA splicing is unaffected in patients. We generated human embryonic stem cells harboring the PN-associated mutation c.531_delA in USB1 and show that this mutation impairs human hematopoiesis. Dysregulated microRNA (miRNA) levels in USB1 mutants during blood development contribute to hematopoietic failure, because of a failure to remove 3'-end adenylated tails added by PAPD5/7. Modulation of miRNA 3'-end adenylation through genetic or chemical inhibition of PAPD5/7 rescues hematopoiesis in USB1 mutants. This work shows that USB1 acts as a miRNA deadenylase and suggests PAPD5/7 inhibition as a potential therapy for PN.
Topics: Humans; Hematopoiesis; Human Embryonic Stem Cells; MicroRNAs; Neutropenia; Phosphoric Diester Hydrolases; Mutation
PubMed: 36862787
DOI: 10.1126/science.abj8379