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Cellular and Molecular Life Sciences :... Sep 2011The human genome contains more than 1,000 microRNA (miRNA) genes, which are transcribed mainly by RNA polymerase II. The canonical pathway of miRNA biogenesis includes... (Review)
Review
The human genome contains more than 1,000 microRNA (miRNA) genes, which are transcribed mainly by RNA polymerase II. The canonical pathway of miRNA biogenesis includes the nuclear processing of primary transcripts (pri-miRNAs) by the ribonuclease Drosha and further cytoplasmic processing of pre-miRNAs by the ribonuclease Dicer. This review discusses the issue of miRNA end heterogeneity generated primarily by Drosha and Dicer cleavage and focuses on the structural aspects of the Dicer step of miRNA biogenesis. We examine the structures of miRNA precursors, both predicted and experimentally determined, as well as the influence of various motifs that disturb the regularity of pre-miRNA structure on Dicer cleavage specificity. We evaluate the structural determinants of the length diversity of miRNA generated by Dicer from different precursors and highlight the importance of asymmetrical motifs. Finally, we discuss the impact of Dicer protein partners on cleavage efficiency and specificity and propose the contribution of pre-miRNA structural plasticity to the dynamics of the dicing complex.
Topics: Humans; MicroRNAs; RNA Precursors; RNA Processing, Post-Transcriptional; Ribonuclease III
PubMed: 21607569
DOI: 10.1007/s00018-011-0726-2 -
Journal of Pharmaceutical and... Jun 2022Let-7e precursor microRNA has the potential to adopt a G-quadruplex (rG4) structure and recently, its roles in oncology have been the focus of much attention, as it is...
Let-7e precursor microRNA has the potential to adopt a G-quadruplex (rG4) structure and recently, its roles in oncology have been the focus of much attention, as it is now known that let-7e pre-miRNA is frequently dysregulated in cancers. Therefore, it is crucial to unveil and fully characterize its ability to adopt a rG4 structure, which could be stabilized or destabilized by small molecules and proteins such as nucleolin, a protein that is deeply associated with miRNA biogenesis. Herein, by combining a set of different methods such as circular dichroism (CD), nuclear magnetic resonance (NMR), UV spectroscopy (thermal difference spectra (TDS) and isothermal difference spectra (IDS)) and polyacrylamide gel electrophoresis (PAGE), we demonstrate the formation of the rG4 structure found in let-7e pre-miRNA sequence in the presence of K (5'-GGGCUGAGGUAGGAGG-3'). The ability of eight small molecules (or ligands) to bind to and stabilize this rG4 structure was also fully assessed. The dissociation constants for each RNA G-quadruplex/ligand complex, determined by surface plasmon resonance (SPR), ranged in the 10 to 10 M range. Lastly, the binding of the rG4 structure to nucleolin in the presence and absence of ligands was evaluated via CD, SPR, PAGE and confocal microscopy. The small molecules 360 A and PDS demonstrated attractive properties to targetthe rG4 structure of let-7e pre-miRNA and control its biology. Our findings also highlighted that the interaction of TMPyP4 with the G-quadruplex of let-7e precursor miRNA could block the formation of the complex between the rG4 and nucleolin. Overall, this study introduces an approach to target the rG4 found in let-7e pre-miRNA which opens up a new opportunity to control the microRNA biogenesis.
Topics: G-Quadruplexes; Ligands; MicroRNAs; Phosphoproteins; RNA-Binding Proteins; Nucleolin
PubMed: 35462282
DOI: 10.1016/j.jpba.2022.114757 -
Scientific Reports Apr 2021The aberrant expression of microRNAs (miRs) has been linked to several human diseases. A promising approach for targeting these anomalies is the use of small-molecule...
The aberrant expression of microRNAs (miRs) has been linked to several human diseases. A promising approach for targeting these anomalies is the use of small-molecule inhibitors of miR biogenesis. These inhibitors have the potential to (i) dissect miR mechanisms of action, (ii) discover new drug targets, and (iii) function as new therapeutic agents. Here, we designed Förster resonance energy transfer (FRET)-labeled oligoribonucleotides of the precursor of the oncogenic miR-21 (pre-miR-21) and used them together with a set of aminoglycosides to develop an interbase-FRET assay to detect ligand binding to pre-miRs. Our interbase-FRET assay accurately reports structural changes of the RNA oligonucleotide induced by ligand binding. We demonstrate its application in a rapid, qualitative drug candidate screen by assessing the relative binding affinity between 12 aminoglycoside antibiotics and pre-miR-21. Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) were used to validate our new FRET method, and the accuracy of our FRET assay was shown to be similar to the established techniques. With its advantages over SPR and ITC owing to its high sensitivity, small sample size, straightforward technique and the possibility for high-throughput expansion, we envision that our solution-based method can be applied in pre-miRNA-target binding studies.
Topics: Aminoglycosides; Fluorescence Resonance Energy Transfer; Humans; Kinetics; MicroRNAs; Protein Binding; Surface Plasmon Resonance
PubMed: 33931703
DOI: 10.1038/s41598-021-88922-0 -
Critical Reviews in Biochemistry and... 2016MicroRNAs (miRNAs) are integral to the gene regulatory network. A single miRNA is capable of controlling the expression of hundreds of protein coding genes and modulate... (Review)
Review
MicroRNAs (miRNAs) are integral to the gene regulatory network. A single miRNA is capable of controlling the expression of hundreds of protein coding genes and modulate a wide spectrum of biological functions, such as proliferation, differentiation, stress responses, DNA repair, cell adhesion, motility, inflammation, cell survival, senescence and apoptosis, all of which are fundamental to tumorigenesis. Overexpression, genetic amplification, and gain-of-function mutation of oncogenic miRNAs ("onco-miRs") as well as genetic deletion and loss-of-function mutation of tumor suppressor miRNAs ("suppressor-miRs") are linked to human cancer. In addition to the dysregulation of a specific onco-miR or suppressor-miRs, changes in global miRNA levels resulting from a defective miRNA biogenesis pathway play a role in tumorigenesis. The function of individual onco-miRs and suppressor-miRs and their target genes in cancer has been described in many different articles elsewhere. In this review, we primarily focus on the recent development regarding the dysregulation of the miRNA biogenesis pathway and its contribution to cancer.
Topics: Animals; Argonaute Proteins; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Humans; MicroRNAs; Neoplasms; Protein Processing, Post-Translational; Ribonuclease III; Transcription, Genetic
PubMed: 26628006
DOI: 10.3109/10409238.2015.1117054 -
European Journal of Pharmaceutical... Feb 2022One of the most significant challenges in capturing and detecting biomarkers is the choice of an appropriate biomolecular receptor. Recently, RNA G-quadruplexes emerged...
One of the most significant challenges in capturing and detecting biomarkers is the choice of an appropriate biomolecular receptor. Recently, RNA G-quadruplexes emerged as plausible receptors due to their ability to recognize with high-affinity proteins. Herein, we have unveiled and characterized the capability of the precursor microRNA 149 to form a G-quadruplex structure and determined the role that some ligands may have in its folding and binding capacity to nucleolin. The G-quadruplex formation was induced by K ions and stabilized by ligands, as demonstrated by nuclear magnetic resonance and circular dichroism experiments. Surface plasmon resonance measurements showed a binding affinity of precursor microRNA 149 towards ligands in the micromolar range (10-10 M) and a strong binding affinity to nucleolin RNA-binding domains 1 and 2 (8.38 × 10 M). Even in the presence of the ligand PhenDC3, the binding remains almost identical and in the same order of magnitude (4.46 × 10 M). The molecular interactions of the RNA G-quadruplex motif found in precursor miRNA 149 (5'-GGGAGGGAGGGACGGG- 3') and nucleolin RNA-binding domains 1 and 2 were explored by means of molecular docking and molecular dynamics studies. The results showed that RNA G-quadruplex binds to a cavity between domains 1 and 2 of the protein. Then, complex formation was also evaluated through polyacrylamide gel electrophoresis. The results suggest that precursor microRNA 149/ligands and precursor microRNA 149/nucleolin RNA-binding domains 1 and 2 form stable molecular complexes. The in vitro co-localization of precursor microRNA 149 and nucleolin in PC3 cells was demonstrated using confocal microscopy. Finally, a rapid and straightforward microfluidic strategy was employed to check the ability of precursor microRNA 149 to capture nucleolin RNA-binding domains 1 and 2. The results revealed that precursor microRNA 149 can capture nucleolin RNA-binding domains 1 and 2 labeled with Fluorescein 5-isothiocyanate in a concentration-dependent manner, but PhenDC3 complexation seems to decrease the ability of precursor microRNA 149 to capture the protein. Overall, our results proved the formation of the G-quadruplex structure in the precursor microRNA 149 and the ability to recognize and detect nucleolin. This proof-of-concept study could open up a new framework for developing new strategies to design improved molecular receptors for capture and detection of nucleolin in complex biological samples.
Topics: Cell Line; G-Quadruplexes; Humans; MicroRNAs; Molecular Docking Simulation; Phosphoproteins; RNA-Binding Proteins; Nucleolin
PubMed: 34922315
DOI: 10.1016/j.ejps.2021.106093 -
Cells Nov 2021In recent years, there has been a large amount of evidence on the role of microRNA (miRNA) in regulating adipose tissue physiology. Indeed, miRNAs control critical steps... (Review)
Review
In recent years, there has been a large amount of evidence on the role of microRNA (miRNA) in regulating adipose tissue physiology. Indeed, miRNAs control critical steps in adipocyte differentiation, proliferation and browning, as well as lipolysis, lipogenesis and adipokine secretion. Overnutrition leads to a significant change in the adipocyte miRNOME, resulting in adipose tissue dysfunction. Moreover, via secreted mediators, dysfunctional adipocytes may impair the function of other organs and tissues. However, given their potential to control cell and whole-body energy expenditure, miRNAs also represent critical therapeutic targets for treating obesity and related metabolic complications. This review attempts to integrate present concepts on the role miRNAs play in adipose tissue physiology and obesity-related dysfunction and data from pre-clinical and clinical studies on the diagnostic or therapeutic potential of miRNA in obesity and its related complications.
Topics: Adipogenesis; Adipokines; Adipose Tissue; Gene Expression Regulation; Humans; Insulin Resistance; MicroRNAs
PubMed: 34943849
DOI: 10.3390/cells10123342 -
Methods (San Diego, Calif.) Jul 2016RNA interference (RNAi) is an extremely useful tool for inhibiting gene expression. It can be triggered by transfected synthetic small interfering RNA (siRNA) or by... (Review)
Review
RNA interference (RNAi) is an extremely useful tool for inhibiting gene expression. It can be triggered by transfected synthetic small interfering RNA (siRNA) or by expressed small hairpin RNA (shRNA). The cellular machinery processes the latter into siRNA in vivo. shRNA is preferred or required in genetic screens and specific RNAi approaches in gene therapy settings. Despite its many successes, the field of shRNAs faces many challenges. Insufficient knockdowns and off-target effects become obstacles for shRNA usage in many applications. Numerous failures are triggered by pitfalls in shRNA design that is often associated with impoverished biogenesis. Here, based on current understanding of the miRNA maturation pathway, we discuss the principles of different shRNA design (pre-miRNA-like, pri-miRNA-like and Ago-shRNA) with an emphasis on the RNA structure. We also provide detailed instructions for an optimal design of pre-miRNA-like shRNA.
Topics: Animals; Base Sequence; Gene Knockdown Techniques; Genetic Therapy; Humans; Inverted Repeat Sequences; MicroRNAs; Promoter Regions, Genetic; RNA Interference; RNA, Small Interfering
PubMed: 27083402
DOI: 10.1016/j.ymeth.2016.04.003 -
Genetics and Molecular Research : GMR Jul 2016MicroRNAs (miRNAs) are a class of small non-coding RNA molecules of about 22 nucleotides in length. miRNAs are highly conserved in both plants and animals, and function... (Review)
Review
MicroRNAs (miRNAs) are a class of small non-coding RNA molecules of about 22 nucleotides in length. miRNAs are highly conserved in both plants and animals, and function as gene regulators by binding to the 3'-untranslated region of target mRNAs for cleavage and/or translational repression. miRNA biogenesis, stability, and regulation of expression are strongly sequence dependent. Sequence variants, such as single nucleotide polymorphisms (SNPs) in pri-miRNA, pre-miRNA, promoter regions, or miRNA-target sites, can influence miRNA function, thereby contributing to the pathological features of human disease. In this review, we focus on miRNA-related SNPs in gastric cancer and comprehensively analyze some commonly studied SNPs.
Topics: Gene Expression Regulation; Genetic Predisposition to Disease; Humans; MicroRNAs; Polymorphism, Single Nucleotide; RNA, Messenger; Stomach Neoplasms
PubMed: 27421013
DOI: 10.4238/gmr.15028289 -
Scientific Reports Jul 2021miRNAs (or microRNAs) are small, endogenous, and noncoding RNAs construct of about 22 nucleotides. Cumulative evidence from biological experiments shows that miRNAs play...
miRNAs (or microRNAs) are small, endogenous, and noncoding RNAs construct of about 22 nucleotides. Cumulative evidence from biological experiments shows that miRNAs play a fundamental and important role in various biological processes. Therefore, the classification of miRNA is a critical problem in computational biology. Due to the short length of mature miRNAs, many researchers are working on precursor miRNAs (pre-miRNAs) with longer sequences and more structural features. Pre-miRNAs can be divided into two groups as mirtrons and canonical miRNAs in terms of biogenesis differences. Compared to mirtrons, canonical miRNAs are more conserved and easier to be identified. Many existing pre-miRNA classification methods rely on manual feature extraction. Moreover, these methods focus on either sequential structure or spatial structure of pre-miRNAs. To overcome the limitations of previous models, we propose a nucleotide-level hybrid deep learning method based on a CNN and LSTM network together. The prediction resulted in 0.943 (%95 CI ± 0.014) accuracy, 0.935 (%95 CI ± 0.016) sensitivity, 0.948 (%95 CI ± 0.029) specificity, 0.925 (%95 CI ± 0.016) F1 Score and 0.880 (%95 CI ± 0.028) Matthews Correlation Coefficient. When compared to the closest results, our proposed method revealed the best results for Acc., F1 Score, MCC. These were 2.51%, 1.00%, and 2.43% higher than the closest ones, respectively. The mean of sensitivity ranked first like Linear Discriminant Analysis. The results indicate that the hybrid CNN and LSTM networks can be employed to achieve better performance for pre-miRNA classification. In future work, we study on investigation of new classification models that deliver better performance in terms of all the evaluation criteria.
Topics: Algorithms; Computational Biology; Deep Learning; Humans; Machine Learning; MicroRNAs; Neural Networks, Computer
PubMed: 34239004
DOI: 10.1038/s41598-021-93656-0 -
Intervirology 2023Herpes simplex virus 1 (HSV-1), an important human pathogen, is capable of latent infection in neurons and productive (lytic) infection in other tissue cells. Once... (Review)
Review
BACKGROUND
Herpes simplex virus 1 (HSV-1), an important human pathogen, is capable of latent infection in neurons and productive (lytic) infection in other tissue cells. Once infected with HSV-1, the immune system of the organism cannot eliminate the virus and carries it lifelong. HSV-1 possesses approximately 150 kb of double-stranded linear genomic DNA and can encode at least 70 proteins and 37 mature microRNAs (miRNAs) derived from 18 precursor miRNAs (pre-miRNAs).
SUMMARY
These HSV-1-encoded miRNAs are widely involved in multiple processes in the life cycle of the virus and the host cell, including viral latent and lytic infection, as well as host cell immune signaling, proliferation, and apoptosis.
KEY MESSAGE
In this review, we focused primarily on recent advances in HSV-1-encoded miRNA expression, function, and mechanism, which may provide new research ideas and feasible research methods systemically and comprehensively.
Topics: Humans; MicroRNAs; Herpesvirus 1, Human; Virus Latency; Signal Transduction
PubMed: 37285807
DOI: 10.1159/000531348