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Journal of Biomedicine & Biotechnology 2009MicroRNAs (miRNAs) are often hosted in introns of protein-coding genes. Given that the same transcriptional unit can potentially give rise to both miRNA and mRNA... (Review)
Review
MicroRNAs (miRNAs) are often hosted in introns of protein-coding genes. Given that the same transcriptional unit can potentially give rise to both miRNA and mRNA transcripts raises the intriguing question of the level of interaction between these processes. Recent studies from transcription, pre-mRNA splicing, and miRNA-processing perspectives have investigated these relationships and yielded interesting, yet somewhat controversial findings. Here we discuss major studies in the field.
Topics: Humans; MicroRNAs; Models, Molecular; RNA Precursors; RNA Splicing; Signal Transduction
PubMed: 19606257
DOI: 10.1155/2009/594678 -
Methods (San Diego, Calif.) Sep 2019microRNAs (miRNAs) are considered as master regulators of biological processes. Dysregulation of miRNA expression has been implicated in many human diseases. Driven by...
microRNAs (miRNAs) are considered as master regulators of biological processes. Dysregulation of miRNA expression has been implicated in many human diseases. Driven by the key biological roles and the therapeutic potential, developing methods for miRNA regulation has become an intense research area. Due to favorable pharmacological properties, small molecule-based miRNA inhibition emerges as a promising strategy and significant progresses have been made. However, it remains challenging to regulate miRNA using small molecules because of the inherent difficulty in RNA targeting and inhibition. Herein we outline the workflow of generating bifunctional small molecule inhibitors blocking miRNA biogenesis through proximity-enabled inactivation of Dicer, an enzyme required for the processing of precursor miRNA (pre-miRNA) into mature miRNA. By conjugating a weak Dicer inhibitor with a pre-miRNA binder, the inhibitor can be delivered to the Dicer processing site associated with the targeted pre-miRNA, and as a result inhibiting Dicer-mediated pre-miRNA processing. This protocol can be applicable in producing bifunctional inhibitors for different miRNAs.
Topics: Enzyme Inhibitors; Gene Expression Regulation; Humans; MicroRNAs; RNA; Ribonuclease III; Small Molecule Libraries
PubMed: 31077820
DOI: 10.1016/j.ymeth.2019.05.004 -
Acta Neuropathologica Communications Jul 2022Altered microRNA (miRNA) expression is a common feature of Huntington's disease (HD) and could participate in disease onset and progression. However, little is known...
Altered microRNA (miRNA) expression is a common feature of Huntington's disease (HD) and could participate in disease onset and progression. However, little is known about the underlying causes of miRNA disruption in HD. We and others have previously shown that mutant Huntingtin binds to Ago2, a central component of miRNA biogenesis, and disrupts mature miRNA levels. In this study, we sought to determine if miRNA maturation per se was compromised in HD. Towards this end, we characterized major miRNA biogenesis pathway components and miRNA maturation products (pri-miRNA, pre-miRNA, and mature) in human HD (N = 41, Vonsattel grades HD2-4) and healthy control (N = 25) subjects. Notably, the striatum (putamen) and cortex (BA39) from the same individuals were analyzed in parallel. We show that Ago2, Drosha, and Dicer were strongly downregulated in human HD at the early stages of the disease. Using a panel of HD-related miRNAs (miR-10b, miR-196b, miR-132, miR-212, miR-127, miR-128), we uncovered various types of maturation defects in the HD brain, the most prominent occurring at the pre-miRNA to mature miRNA maturation step. Consistent with earlier findings, we provide evidence that alterations in autophagy could participate in miRNA maturation defects. Notably, most changes occurred in the striatum, which is more prone to HTT aggregation and neurodegeneration. Likewise, we observed no significant alterations in miRNA biogenesis in human HD cortex and blood, strengthening tissue-specific effects. Overall, these data provide important clues into the underlying mechanisms behind miRNA alterations in HD-susceptible tissues. Further investigations are now required to understand the biological, diagnostic, and therapeutic implications of miRNA/RNAi biogenesis defects in HD and related neurodegenerative disorders.
Topics: Brain; Corpus Striatum; Humans; Huntingtin Protein; Huntington Disease; MicroRNAs; Putamen
PubMed: 35869509
DOI: 10.1186/s40478-022-01407-7 -
BioMed Research International 2021Single nucleotide polymorphisms (SNPs) play a significant role in microRNA (miRNA) generation, processing, and function and contribute to multiple phenotypes and...
Single nucleotide polymorphisms (SNPs) play a significant role in microRNA (miRNA) generation, processing, and function and contribute to multiple phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect miRNA maturation mechanisms is important for precision medicine. The present study established an SNP-associated pre-miRNA (SNP-pre-miRNA) database, named miRSNPBase, and constructed SNP-pre-miRNA sequences. We also identified phenotypes and disease biomarker-associated isoform miRNA (isomiR) based on miRFind, which was developed in our previous study. We identified functional SNPs and isomiRs. We analyzed the biological characteristics of functional SNPs and isomiRs and studied their distribution in different ethnic groups using whole-genome analysis. Notably, we used individuals from Great Britain (GBR) as examples and identified isomiRs and isomiR-associated SNPs (iso-SNPs). We performed sequence alignments of isomiRs and miRNA sequencing data to verify the identified isomiRs and further revealed GBR ethnographic epigenetic dominant biomarkers. The SNP-pre-miRNA database consisted of 886 pre-miRNAs and 2640 SNPs. We analyzed the effects of SNP type, SNP location, and SNP-mediated free energy change during mature miRNA biogenesis and found that these factors were closely associated to mature miRNA biogenesis. Remarkably, 158 isomiRs were verified in the miRNA sequencing data for the 18 GBR samples. Our results indicated that SNPs affected the mature miRNA processing mechanism and contributed to the production of isomiRs. This mechanism may have important significance for epigenetic changes and diseases.
Topics: Biomarkers; Databases, Genetic; Epigenesis, Genetic; Gene Expression Profiling; Genome; Genome-Wide Association Study; Genotype; High-Throughput Nucleotide Sequencing; Humans; MicroRNAs; Models, Genetic; Phenotype; Polymorphism, Single Nucleotide
PubMed: 34239922
DOI: 10.1155/2021/2403418 -
PloS One 2017MicroRNA play an important role in post-transcriptional regulation of most transcripts in the human genome, but their evolution across the primate lineage is largely...
MicroRNA play an important role in post-transcriptional regulation of most transcripts in the human genome, but their evolution across the primate lineage is largely uncharacterized. A particular miRNA can have one to thousands of messenger RNA targets, establishing the potential for a small change in sequence or overall miRNA structure to have profound phenotypic effects. However, the majority of non-human primate miRNA is predicted solely by homology to the human genome and lacks experimental validation. In the present study, we sequenced thirteen species representing a wide range of the primate phylogeny. Hundreds of miRNA were validated, and the number of species with experimentally validated miRNA was tripled. These species include a sister taxon to humans (bonobo) and basal primates (aye-aye, mouse lemur, galago). Consistent with previous studies, we found the seed region and mature miRNA to be highly conserved across primates, with overall structural conservation of the pre-miRNA hairpin. However, there were a number of interesting exceptions, including a seed shift due to structural changes in miR-501. We also identified an increase in the number of miR-320 paralogs throughout primate evolution. Many of these non-conserved miRNA appear to regulate neuronal processes, illustrating the importance of investigating miRNA to learn more about human evolution.
Topics: Animals; Base Sequence; Evolution, Molecular; Genetic Variation; MicroRNAs; Primates
PubMed: 28640911
DOI: 10.1371/journal.pone.0176596 -
Journal of Animal Science Apr 2009Posttranscriptional gene regulation plays a vital role in male and female germ cell function, but our understanding of this regulatory process in somatic cells and its... (Review)
Review
Posttranscriptional gene regulation plays a vital role in male and female germ cell function, but our understanding of this regulatory process in somatic cells and its effect on reproductive tissue development and function is not understood. In mammalian cells, microRNA (miRNA) are key posttranscriptional regulators and function by modulating translation or degradation of their target mRNA. Mature miRNA are synthesized through a multi-step process that concludes with the cleavage of stem-loop pre-miRNA by the RNase III enzyme, Dicer1. To determine the extent of miRNA regulation and establish a baseline, miRNA profiling has indicated the presence of large numbers of miRNA within reproductive tissues and cells. Moreover, several studies have indicated that miRNA expression in reproductive tissues varies in response to pituitary and gonadal hormones. To understand the role that miRNA-mediated posttranscriptional gene regulation plays in female reproduction, a global Dicer1 hypomorph mouse and several tissue-specific Dicer1 knockout mice have been studied. Interestingly, when Dicer1 expression is decreased in reproductive tissues or cells, the females are infertile. This review discusses all the work regarding miRNA regulation within the mammalian female reproductive system published to date.
Topics: Animals; Female; Genital Diseases, Female; Genitalia, Female; MicroRNAs; Zygote
PubMed: 18791135
DOI: 10.2527/jas.2008-1331 -
Nature Communications Apr 2022The accurate and efficient cleavage of shRNAs and pre-miRNAs by DICER is crucial for their gene-silencing activity. Here, we conduct high-throughput DICER cleavage...
The accurate and efficient cleavage of shRNAs and pre-miRNAs by DICER is crucial for their gene-silencing activity. Here, we conduct high-throughput DICER cleavage assays for more than ~20,000 different shRNAs and show the comprehensive cleavage activities of DICER on these sequences. We discover a single-nucleotide bulge (22-bulge), which facilitates the cleavage activity of DICER on shRNAs and human pre-miRNAs. As a result, this 22-bulge enhances the gene-silencing activity of shRNAs and the accuracy of miRNA biogenesis. In addition, various single-nucleotide polymorphism-edited 22-bulges are found to govern the cleavage sites of DICER on pre-miRNAs and thereby control their functions. Finally, we identify the single cleavage of DICER and reveal its molecular mechanism. Our findings improve the understanding of the DICER cleavage mechanism, provide a foundation for the design of accurate and efficient shRNAs for gene-silencing, and indicate the function of bulges in regulating miRNA biogenesis.
Topics: Humans; Gene Silencing; MicroRNAs; Ribonuclease III; RNA Precursors; RNA, Small Interfering; Polymorphism, Single Nucleotide
PubMed: 35440644
DOI: 10.1038/s41467-022-29822-3 -
Genes Aug 2021MicroRNAs (miRNAs) are a kind of short non-coding ribonucleic acid molecules that can regulate gene expression. The computational identification of plant miRNAs is of...
MicroRNAs (miRNAs) are a kind of short non-coding ribonucleic acid molecules that can regulate gene expression. The computational identification of plant miRNAs is of great significance to understanding biological functions. In our previous studies, we have put firstly forward and further developed a set of knowledge-based energy features to construct two plant pre-miRNA prediction tools (plantMirP and riceMirP). However, these two tools cannot be used for miRNA prediction from NGS (Next-Generation Sequencing) data. In addition, for further improving the prediction performance and accessibility, plantMirP2 has been developed. Based on the latest dataset, plantMirP2 achieves a promising performance: 0.9968 (Area Under Curve, AUC), 0.9754 (accuracy), 0.9675 (sensitivity) and 0.9876 (specificity). Additionally, the comparisons with other plant pre-miRNA tools show that plantMirP2 performs better. Finally, the webserver and stand-alone version of plantMirP2 are available.
Topics: Algorithms; Computational Biology; MicroRNAs; Plants; RNA Precursors; Software; Support Vector Machine
PubMed: 34440454
DOI: 10.3390/genes12081280 -
International Journal of Molecular... Jan 2023MicroRNAs (miRNAs), playing an important role in cell differentiation, development, gene regulation, and apoptosis, have attracted much attention in recent years. miRNAs...
MicroRNAs (miRNAs), playing an important role in cell differentiation, development, gene regulation, and apoptosis, have attracted much attention in recent years. miRNAs were shown to be involved in the mechanisms of various diseases, and certainly, they can be employed as useful disease biomarkers. The phylogenetic tree analysis of miRNA biomarkers is a useful tool to investigate the association between various diseases as well as the association between viruses and disease. In addition to the phylogenetic tree analysis, a more advanced study is to use the miRNA distance distribution to evaluate the similarity of the miRNA biomarkers. The mature miRNA distance distribution based on mature miRNA sequences has been derived. The averages of the pairwise distances of miRNA biomarkers for several associated diseases were shown to be smaller than the overall mean of all miRNAs, which indicates the high similarity of miRNA biomarkers for associated diseases. In addition to the mature miRNA, the precursor miRNA (pre-miRNA) may be more useful to explore the similarity of miRNAs because the mature miRNA duplex is released from the pre-miRNA. Therefore, in this study, the distance distributions based on human pre-miRNA stem-loop sequences were derived. The 1917 human miRNA stem-loop sequences in the miRBase dataset were used to derive the pre-miRNA distance distribution, and this is the first study to provide the distance distribution based on the human pre-miRNAs. The similarity of miRNA biomarkers for several associated diseases or vaccines was examined using the derived distribution, and the results show that the similarity of pre-miRNA biomarkers may be a feasible way to help explore the disease association.
Topics: Humans; MicroRNAs; Phylogeny; Gene Expression Regulation; Biomarkers; Cell Differentiation
PubMed: 36674554
DOI: 10.3390/ijms24021009 -
RNA (New York, N.Y.) May 2014microRNAs (miRNAs) are crucial for cellular development and homeostasis. In order to better understand regulation of miRNA biosynthesis, we studied cleavage of primary...
microRNAs (miRNAs) are crucial for cellular development and homeostasis. In order to better understand regulation of miRNA biosynthesis, we studied cleavage of primary miRNAs by Drosha. While Drosha knockdown triggers an expected decrease of many mature miRNAs in human embryonic stem cells (hESC), a subset of miRNAs are not reduced. Statistical analysis of miRNA secondary structure and fold change of expression in response to Drosha knockdown showed that absence of mismatches in the central region of the hairpin, 5 and 9-12 nt from the Drosha cutting site conferred decreased sensitivity to Drosha knockdown. This suggests that, when limiting, Drosha processes miRNAs without mismatches more efficiently than mismatched miRNAs. This is important because Drosha expression changes over cellular development and the fold change of expression for miRNAs with mismatches in the central region correlates with Drosha levels. To examine the biochemical relationship directly, we overexpressed structural variants of miRNA-145, miRNA-137, miRNA-9, and miRNA-200b in HeLa cells with and without Drosha knockdown; for these miRNAs, elimination of mismatches in the central region increased, and addition of mismatches decreased their expression in an in vitro assay and in cells with low Drosha expression. Change in Drosha expression can be a biologically relevant mechanism by which eukaryotic cells control miRNA profiles. This phenomenon may explain the impact of point mutations outside the seed region of certain miRNAs.
Topics: Gene Expression Regulation; HeLa Cells; Humans; MicroRNAs; Nucleic Acid Conformation; Point Mutation; Ribonuclease III
PubMed: 24677349
DOI: 10.1261/rna.043943.113