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Cellular and Molecular Life Sciences :... Jan 2015microRNAs (miRNAs) are important regulators of gene expression. After excised from primary miRNA transcript by dicer-like1 (DCL1, an RNAse III enzyme), miRNAs bind and... (Review)
Review
microRNAs (miRNAs) are important regulators of gene expression. After excised from primary miRNA transcript by dicer-like1 (DCL1, an RNAse III enzyme), miRNAs bind and guide their effector protein named argonaute 1 (AGO1) to silence the expression of target RNAs containing their complementary sequences in plants. miRNA levels and activities are tightly controlled to ensure their functions in various biological processes such as development, metabolism and responses to abiotic and biotic stresses. Studies have identified many factors that involve in miRNA accumulation and activities. Characterization of these factors in turn greatly improves our understanding of the processes related to miRNAs. Here, we review recent progress of mechanisms underlying miRNA expression and functions in plants.
Topics: Gene Expression Regulation, Plant; Genes, Plant; MicroRNAs; Plants
PubMed: 25209320
DOI: 10.1007/s00018-014-1728-7 -
Balkan Medical Journal Feb 2020Cardiovascular diseases are one of the most common causes of death in both developing and developed countries worldwide. Even though there have been improvements in...
Cardiovascular diseases are one of the most common causes of death in both developing and developed countries worldwide. Even though there have been improvements in primary prevention, the prevalence of cardiovascular diseases continues to increase in recent years. Hence, it is crucial to both investigate the molecular pathophysiology of cardiovascular diseases in-depth and find novel biomarkers regarding the early and proper prevention and diagnosis of these diseases. MicroRNAs, or miRNAs, are endogenous, conserved, single-stranded non-coding RNAs of 21-25 nucleotides in length. miRNAs have important roles in various cellular events such as embryogenesis, proliferation, vasculogenesis, apoptosis, cell growth, differentiation, and tumorigenesis. They also have potential roles in the cardiovascular system, including angiogenesis, cardiac cell contractility, control of lipid metabolism, plaque formation, the arrangement of cardiac rhythm, and cardiac cell growth. Circulating miRNAs are promising novel biomarkers for purposes of the diagnosis and prognosis of cardiovascular diseases. Cell or tissue specificity, stability in serum or plasma, resistance to degradative factors such as freeze-thaw cycles or enzymes in the blood, and fast-release kinetics, provide the potential for miRNAs to be surrogate markers for the early and accurate diagnosis of disease and for predicting middle- or long-term prognosis. Moreover, it may be a logical approach to combine miRNAs with traditional biomarkers to improve risk stratification and long-term prognosis. In addition to their efficacy in both diagnosis and prognosis, miRNA-based therapeutics may be beneficial for treating cardiovascular diseases using novel platforms and computational tools and in combination with traditional methods of analysis. microRNAs are promising, novel therapeutic agents, which can affect multiple genes using different signaling pathways. miRNAs therapeutic modulation techniques have been used in the settings of atherosclerosis, acute myocardial infarction, restenosis, vascular remodeling, arrhythmias, hypertrophy and fibrosis, angiogenesis and cardiogenesis, aortic aneurysm, pulmonary hypertension, and ischemic injury. This review presents detailed information about miRNAs regarding structure and biogenesis, stages of synthesis and functions, expression profiles in serum/plasma of living organisms, diagnostic and prognostic potential as novel biomarkers, and therapeutic applications in various diseases.
Topics: Biomarkers; Cardiovascular Diseases; Humans; MicroRNAs; Prognosis
PubMed: 32018347
DOI: 10.4274/balkanmedj.galenos.2020.2020.1.94 -
BMC Bioinformatics May 2023One strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However,...
BACKGROUND
One strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However, distinguishing direct targets from secondary effects and experimental noise can be challenging when confounding signal is present in the background at varying levels.
RESULTS
Here, we present a statistical modeling strategy to identify microRNAs that are primary substrates of target-directed miRNA degradation (TDMD) mediated by ZSWIM8. This method uses a bi-beta-uniform mixture (BBUM) model to separate primary from background signal components, leveraging the expectation that primary signal is restricted to upregulation and not downregulation upon loss of ZSWIM8. The BBUM model strategy retained the apparent sensitivity and specificity of the previous ad hoc approach but was more robust against outliers, achieved a more consistent stringency, and could be performed using a single cutoff of false discovery rate (FDR).
CONCLUSIONS
We developed the BBUM model, a robust statistical modeling strategy to account for background secondary signal in differential expression data. It performed well for identifying primary substrates of TDMD and should be useful for other applications in which the primary regulatory targets are only upregulated or only downregulated. The BBUM model, FDR-correction algorithm, and significance-testing methods are available as an R package at https://github.com/wyppeter/bbum .
Topics: MicroRNAs; Algorithms; Base Sequence; Models, Statistical; Sequence Analysis, RNA; High-Throughput Nucleotide Sequencing
PubMed: 37170259
DOI: 10.1186/s12859-023-05306-z -
Journal of Neurochemistry Nov 2012In a previous study, we reported that microRNA (miRNA) precursors are expressed in synaptic fractions within adult mouse forebrain, where they are enriched at...
In a previous study, we reported that microRNA (miRNA) precursors are expressed in synaptic fractions within adult mouse forebrain, where they are enriched at post-synaptic densities (PSDs). However, because that study employed qRT-PCR primers that recognize the hairpin region, it was not able to distinguish between primary microRNA gene transcripts (pri-miRs) and small hairpin precursors (pre-miRs). Here, using primer sets that selectively measure regions upstream, downstream and flanking the hairpin, we demonstrate that pri-miRs are present in synaptic fractions (enriched several-fold relative to total tissue homogenate) and are especially enriched in isolated PSDs. Drosha and DGCR8 proteins are also expressed in synaptic fractions and PSDs, and are tightly associated with pri-miRs as assessed by coimmunoprecipitation under stringent conditions. Pri-miRs, drosha, and DGCR8 are highly enriched in fractions that contain mRNA transport particles, and cytosolic drosha is associated with kinesin heavy chain; these findings suggest that pri-miRs are transported to synaptic regions in a manner similar to mRNAs. This study supports the notion that miRNA biogenesis occurs locally near synapses in a regulated fashion.
Topics: Animals; Immunoprecipitation; Male; Mice; Mice, Inbred C57BL; MicroRNAs; Neurons; Phosphopyruvate Hydratase; Post-Synaptic Density; Prosencephalon; Proteins; RNA, Messenger; RNA-Binding Proteins; Ribonuclease III; Synaptosomes
PubMed: 22897173
DOI: 10.1111/j.1471-4159.2012.07921.x -
Cancer Research Mar 2015miRNAs are important regulatory elements for gene expression that are involved in diverse physiologic and pathologic processes. Canonical miRNA biogenesis consists of a... (Review)
Review
miRNAs are important regulatory elements for gene expression that are involved in diverse physiologic and pathologic processes. Canonical miRNA biogenesis consists of a two-step processing, from primary transcripts (pri-miRNA) to precursor miRNAs (pre-miRNA) mediated by Drosha in the nucleus and from pre-miRNAs to mature miRNAs mediated by Dicer in the cytoplasm. Various routes of miRNA maturation that are tightly regulated by signaling cascades and specific to an individual or a subclass of miRNAs have been recently identified. Here, we review the current findings in signaling-mediated miRNA processing as well as their potential clinical relevance in cancer.
Topics: Animals; Gene Expression; Humans; MicroRNAs; Neoplasms; Signal Transduction
PubMed: 25660948
DOI: 10.1158/0008-5472.CAN-14-2568 -
Acta Biochimica Polonica 2016MicroRNAs are short molecules of 21-24 nt in length. They are present in all eukaryotic organisms and regulate gene expression by guiding posttranscriptional silencing...
MicroRNAs are short molecules of 21-24 nt in length. They are present in all eukaryotic organisms and regulate gene expression by guiding posttranscriptional silencing of mRNAs. In plants, they are key players in signal transduction, growth and development, and in response to abiotic and biotic stresses. Barley (Hordeum vulgare) is an economically important monocotyledonous crop plant. Drought is the world's main cause of loss in cereal production. We have constructed a high-throughput Real-Time RT-qPCR platform for parallel determination of 159 barley primary microRNAs' levels. The platform was tested for two drought-and-rehydration-treated barley genotypes (Rolap and Sebastian). We have determined changes in the expression of primary microRNAs responding to mild drought, severe drought, and rehydration. Based on the results obtained, we conclude that alteration in the primary microRNA expression is relative to the stress's intensity. Mild drought and rehydration mostly decrease the pri-miRNA levels in both of the tested genotypes. Severe drought mainly induces the primary microRNA expression. The main difference between the genotypes tested was a much-stronger induction of pri-miRNAs in Rolap encountering severe drought. The primary microRNAs respond dynamically to mild drought, severe drought, and rehydration treatments. We propose that some of the individual pri-miRNAs could be used as drought stress or rehydration markers. The usage of the platform in biotechnology is also postulated.
Topics: Dehydration; Droughts; Gene Expression; Gene Expression Regulation, Plant; Hordeum; MicroRNAs; RNA, Plant; Soil; Stress, Physiological; Water
PubMed: 27770573
DOI: 10.18388/abp.2016_1352 -
Experimental Hematology Jun 2018Acute myeloid leukemia (AML) arises when immature myeloid blast cells acquire multiple, recurrent genetic and epigenetic changes that result in dysregulated... (Comparative Study)
Comparative Study Review
Acute myeloid leukemia (AML) arises when immature myeloid blast cells acquire multiple, recurrent genetic and epigenetic changes that result in dysregulated proliferation. Acute leukemia is the most common form of pediatric cancer, with AML accounting for ~20% of all leukemias in children. The genomic aberrations that drive AML inhibit myeloid differentiation and activate signal transduction pathways that drive proliferation. MicroRNAs, a class of small (~22 nucleotide) noncoding RNAs that posttranscriptionally suppress the expression of specifically targeted transcripts, are also frequently dysregulated in AML, which may prove useful for the purposes of disease classification, prognosis, and future therapeutic approaches. MicroRNA expression profiles are associated with patient prognosis and responses to standard chemotherapy, including predicting therapy resistance in AML. miR-155 is the primary focus of this review because it has been repeatedly associated with poorer survival across multiple cohorts of adult and pediatric AML. We discuss some novel features of miR-155 expression in AML, in particular how the levels of expression can critically influence function. Understanding the role of microRNAs in AML and the ways in which microRNA expression influences AML biology is one means to develop novel and more targeted therapies.
Topics: Adult; Animals; Child; Gene Expression Regulation, Leukemic; Gene Regulatory Networks; Humans; Inflammation; Leukemia, Myeloid, Acute; Mice; MicroRNAs; Phenotype; Prognosis; RNA, Neoplasm; Transcription, Genetic; Transcriptome; Tumor Burden
PubMed: 29601851
DOI: 10.1016/j.exphem.2018.03.007 -
Nature Communications Apr 2020MicroRNAs (miRNAs) are small RNAs that regulate gene expression. miRNAs are produced from primary miRNAs (pri-miRNAs), which are cleaved by Microprocessor....
MicroRNAs (miRNAs) are small RNAs that regulate gene expression. miRNAs are produced from primary miRNAs (pri-miRNAs), which are cleaved by Microprocessor. Microprocessor, therefore, plays a crucial role in determining the efficiency and precision of miRNA production, and thus the function of the final miRNA product. Here, we conducted high-throughput enzymatic assays to investigate the catalytic mechanism of Microprocessor cleaving randomized pri-miRNAs. We identified multiple mismatches and wobble base pairs in the upper stem of pri-miRNAs, which influence the efficiency and accuracy of their processing. The existence of these RNA elements helps to explain the alternative cleavage of Microprocessor for some human pri-miRNAs. We also demonstrated that miRNA biogenesis can be altered via modification of the RNA elements by RNA-editing events or single nucleotide polymorphisms (SNPs). These findings improve our understanding of pri-miRNA processing mechanisms and provide a foundation for interpreting differential miRNA expression due to RNA modifications and SNPs.
Topics: Base Pairing; Gene Expression; HCT116 Cells; HEK293 Cells; Humans; MicroRNAs; Nucleic Acid Conformation; Polymorphism, Single Nucleotide; RNA Editing; RNA Interference; RNA Processing, Post-Transcriptional; RNA-Binding Proteins; Recombinant Proteins; Ribonuclease III; Sequence Analysis, RNA
PubMed: 32317642
DOI: 10.1038/s41467-020-15674-2 -
RNA Biology Aug 2021One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously...
One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously and at similar levels from a common long noncoding transcript. Investigating the two tissue types where C19MC is exclusively expressed, we could show that there is a tissue-specific and chromosomal position-dependent decrease in mature miRNA levels towards the 3' end of the cluster in embryonic stem cells but not in placenta. Although C19MC transcription level is significantly lower in stem cells, this gradual decrease is not present at the primary miRNA levels, indicating that a difference in posttranscriptional processing could explain this observation. By depleting Drosha, the nuclease component of the Microprocessor complex, we could further enhance the positional decrease in stem cells, demonstrating that a tissue-specific, local availability of the Microprocessor complex could lie behind the phenomenon. Moreover, we could describe a tissue-specific promoter being exclusively active in placenta, and the epigenetic mark analysis suggested the presence of several putative enhancer sequences in this region. Performing specific chromatin immunoprecipitation followed by quantitative real-time PCR experiments we could show a strong association of Drosha with selected enhancer regions in placenta, but not in embryonic stem cells. These enhancers could provide explanation for a more efficient co-transcriptional recruitment of the Microprocessor, and therefore a more efficient processing of pri-miRNAs throughout the cluster in placenta. Our results point towards a new model where tissue-specific, posttranscriptional 'fine-tuning' can differentiate among miRNAs that are expressed simultaneously from a common precursor.
Topics: Cell Line, Tumor; Chromosomes, Human, Pair 19; Enhancer Elements, Genetic; Epigenesis, Genetic; Female; Human Embryonic Stem Cells; Humans; MicroRNAs; Multigene Family; Organ Specificity; Placenta; Pregnancy; RNA Precursors; RNA Processing, Post-Transcriptional; Ribonuclease III; Transcription, Genetic
PubMed: 33052778
DOI: 10.1080/15476286.2020.1836457 -
RNA Biology 2014MicroRNAs (miRNAs) are ubiquitous gene regulators that modulate essential cellular processes at the post-transcriptional level. In metazoans and their viruses, most... (Review)
Review
MicroRNAs (miRNAs) are ubiquitous gene regulators that modulate essential cellular processes at the post-transcriptional level. In metazoans and their viruses, most miRNAs are produced from hairpin-containing primary transcripts that are sequentially cleaved by nuclear Drosha and cytoplasmic Dicer. In the last decade, alternative mechanisms that bypass either the Drosha or Dicer cleavage step have emerged, increasing the complexity of the miRNA regulatory network. Here, we highlight non-canonical pathways that generate miRNAs using a variety of molecular machineries that play fundamental roles in the biogenesis and processing of other classes of cellular RNAs.
Topics: Animals; MicroRNAs; RNA Caps; RNA Precursors; RNA Processing, Post-Transcriptional; Ribonuclease III; Transcription, Genetic; Viruses
PubMed: 24823351
DOI: 10.4161/rna.28985