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Elucidating the Role of microRNAs in Cancer Through Data Mining Techniques. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 774:291-315. [DOI: 10.1007/978-94-007-5590-1_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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202
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Schmitz U, Wolkenhauer O. Web resources for microRNA research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 774:225-50. [PMID: 23377976 DOI: 10.1007/978-94-007-5590-1_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the last decade thousands of microRNAs (miRNAs) have been discovered in all kinds of taxa. The ever growing number of identified miRNA genes required ordered cataloging and annotation. This has led to the development of miRNA web resources.MiRNA web resources can be referred to either as web accessible databases (repositories) or web applications that provide a defined computational task upon user request. Today, more than three dozen web accessible resources exist that gather, organize and annotate all kinds of miRNA related data. According to the type of data or data processing method, these miRNA web resources can be classified as miRNA sequence and annotation databases, resources and tools for predicted as well as experimentally validated targets, databases of miRNA regulation and expression, functional annotation and mapping databases and a number of other tools and resources that are species-specific or focus on particular phenotypes.This chapter provides an overview of the different types of miRNA web resources and their purpose and gives some examples for each category. Furthermore, some valuable miRNA web applications will be introduced. Finally, strategies for miRNA data retrieval and associated risks and pitfalls will be discussed.
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Affiliation(s)
- Ulf Schmitz
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
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203
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Abstract
MicroRNAs (miRNAs) are 19-25 nucleotides non-coding RNAs known to have important post-transcriptional regulatory functions. The computational target prediction algorithm is vital to effective experimental testing. However, since different existing algorithms rely on different features and classifiers, there is a poor agreement among the results of different algorithms. To benefit from the advantages of different algorithms, we proposed an algorithm called BCmicrO that combines the prediction of different algorithms with Bayesian Network. BCmicrO was evaluated using the training data and the proteomic data. The results show that BCmicrO improves both the sensitivity and the specificity of each individual algorithm. All the related materials including genome-wide prediction of human targets and a web-based tool are available at http://compgenomics.utsa.edu/gene/gene_1.php.
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Affiliation(s)
- Dong Yue
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - Maozu Guo
- Department of Computer Science and Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yidong Chen
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Yufei Huang
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas 78249, USA
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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204
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Zabaleta J. MicroRNA: A Bridge from H. pylori Infection to Gastritis and Gastric Cancer Development. Front Genet 2012; 3:294. [PMID: 23248648 PMCID: PMC3521996 DOI: 10.3389/fgene.2012.00294] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/28/2012] [Indexed: 12/14/2022] Open
Abstract
Helicobacter pylori (H. pylori) infection is a recognized risk factor for gastric cancer. The disease is one of the most common in the world and explains for a significant number of cancer cases and cancer-associated deaths worldwide. H. pylori infection induces huge array of responses at the gastric epithelial cells and the immune system, inducing both pro- and anti-inflammatory molecules that are intended to either perpetuate or control the infection. Despite the strong immune response, the infection is not cleared and can persist mostly without causing major significant discomfort in the human host. Among the mediators induced in response to the infection, microRNA (miRNA) have the potential to play a major impact on the outcome of the bacteria-host interaction. These miRNA are small 18-24 nucleotide long nucleotide molecules that can interact with mRNA molecules and block their translation into proteins or induce their degradation. Many efforts have been put into the generation of miRNA profiles and their role in gastric cancer. This has led to the identification of miRNA associated with promoting the inflammatory response initiated by the H. pylori infection, increasing the malignant progression of the gastric epithelium, and enhancing the invasiveness and migratory capacity of cancer cells. However, at the same time, several miRNA have been associated with events that are totally opposite, leading to reduced inflammation, inhibition of malignancy and increased apoptosis of transformed cells. In summary, as it is in many other examples, the role played by miRNA in gastric cancer is the results of a delicate balance between pro- and anti-cancer miRNA, and this balance is modified by the interaction of many players, many of which are still waiting to be discovered.
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Affiliation(s)
- Jovanny Zabaleta
- Department of Pediatrics, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center New Orleans, LA, USA
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205
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White K, Loscalzo J, Chan SY. Holding our breath: The emerging and anticipated roles of microRNA in pulmonary hypertension. Pulm Circ 2012; 2:278-90. [PMID: 23130098 PMCID: PMC3487298 DOI: 10.4103/2045-8932.101395] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Over the past decade, the importance of non-coding RNA such as microRNA has been established in numerous processes that drive human pathogenesis. These crucial molecular regulators modulate networks of target gene transcripts that, in turn, orchestrate cellular phenotypes such as cell survival, differentiation, proliferation, and metabolism among others and thus affect cardiopulmonary vascular disease conditions. Many of these same pathophenotypes figure prominently in the complex pathogenesis of pulmonary hypertension, an enigmatic vascular disorder characterized by a histological panvasculopathy and driven by disparate upstream triggers such as hypoxia, inflammation, and bone morphogenetic protein signaling. Yet, the importance of just a few microRNAs in pulmonary hypertension has been recognized, and we are only beginning to understand the integrative functions of these molecules in this disease. By combining systems biology with traditional experimental approaches, more direct insight into the pleiotropy of microRNA should not only further reveal the spectrum of molecular pathways that cause pulmonary hypertension, but also offer novel and much needed diagnostic and therapeutic strategies.
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Affiliation(s)
- Kevin White
- Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
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206
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Takahashi M, Sung B, Shen Y, Hur K, Link A, Boland CR, Aggarwal BB, Goel A. Boswellic acid exerts antitumor effects in colorectal cancer cells by modulating expression of the let-7 and miR-200 microRNA family. Carcinogenesis 2012; 33:2441-9. [PMID: 22983985 PMCID: PMC3510738 DOI: 10.1093/carcin/bgs286] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 08/06/2012] [Accepted: 09/10/2012] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is a complex disease with genetic and epigenetic alterations in many key oncogenes and tumor suppressor genes. The active principle of a gum resin from Boswellia serrata, 3-acetyl-11-keto-β-boswellic acid (AKBA), has recently gained attention as a chemopreventive compound due to its ability to target key oncogenic proteins such as 5-lipoxygenase and nuclear factor-kappaB. AKBA has been shown to inhibit the growth of CRC cells; however, the precise molecular mechanisms underlying its anticancer activities in CRC remain unclear. We hypothesized that boswellic acids may achieve their chemopreventive effects by modulating specific microRNA (miRNA) pathways. We found that AKBA significantly up-regulated expression of the let-7 and miR-200 families in various CRC cell lines. Both let-7 and miR-200 are putative tumor-suppressive miRNAs. AKBA modulated the expression of several downstream targets of the let-7 and miR-200 families, such as CDK6, vimentin and E-cadherin. These data were further strengthened by miRNA knockdown studies, which revealed that inhibition of let-7i facilitated enhanced cancer cell proliferation, migration and invasion. In addition, AKBA also induced similar modulation of the let-7 and miR-200 downstream genes in CRC tumors orthotopically implanted in nude mice. These results indicate that AKBA-induced antitumor effects in CRC occur, at least partly through the up-regulation of specific miRNA pathways. Our data provide novel evidence that anticancer effects of boswellic acids are due in part to their ability to regulate cellular epigenetic machinery and further highlight the promise for this phytochemical in the preventative and therapeutic applications of CRC.
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Affiliation(s)
- Masanobu Takahashi
- GI Cancer Research Laboratory, Baylor University Medical Center, 3500 Gaston Avenue, 250 Hoblitzelle, Dallas, TX 75246, USA
| | - Bokyung Sung
- Department of Experimental Therapeutics, Cytokine Research Laboratory, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Yan Shen
- GI Cancer Research Laboratory, Baylor University Medical Center, 3500 Gaston Avenue, 250 Hoblitzelle, Dallas, TX 75246, USA
| | - Keun Hur
- GI Cancer Research Laboratory, Baylor University Medical Center, 3500 Gaston Avenue, 250 Hoblitzelle, Dallas, TX 75246, USA
| | - Alexander Link
- GI Cancer Research Laboratory, Baylor University Medical Center, 3500 Gaston Avenue, 250 Hoblitzelle, Dallas, TX 75246, USA
| | - C. Richard Boland
- GI Cancer Research Laboratory, Baylor University Medical Center, 3500 Gaston Avenue, 250 Hoblitzelle, Dallas, TX 75246, USA
| | - Bharat B. Aggarwal
- Department of Experimental Therapeutics, Cytokine Research Laboratory, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Ajay Goel
- GI Cancer Research Laboratory, Baylor University Medical Center, 3500 Gaston Avenue, 250 Hoblitzelle, Dallas, TX 75246, USA
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207
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Zhang J, Xie S, Ma W, Teng Y, Tian Y, Huang X, Zhang Y. A newly identified microRNA, mmu-miR-7578, functions as a negative regulator on inflammatory cytokines tumor necrosis factor-α and interleukin-6 via targeting Egr1 in vivo. J Biol Chem 2012. [PMID: 23184950 DOI: 10.1074/jbc.m112.351197] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Appropriate innate immune responses are required to protect an organism against foreign pathogens, and the immune response must be tightly controlled. Here, we report a new microRNA (miRNA) identified from a small RNA library from the epididymis, termed miR-7578, that acts as a negative regulator of inflammatory responses. It was abundantly expressed in immune-related organs and induced by lipopolysaccharide in the lung and epididymis, as well as macrophages stimulated with diverse Toll-like receptor ligands, in an NF-κB-dependent manner. mmu-miR-7578 inhibited the release of pro-inflammatory cytokines, including TNFα and IL6, by regulating its target gene Egr1, which encodes a transcription factor that activates TNFα and NF-κB expression. Transgenic mice overexpressing mmu-miR-7578 displayed higher resistance to endotoxin shock and lower plasma levels of TNFα and IL6, indicating that this miRNA acted as a negative molecule of immune response. In sum, we report a previously uncharacterized LPS-responsive miRNA that controls inflammatory response in a feedback loop by fine-tuning a key transcription factor in vivo.
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Affiliation(s)
- Jinsong Zhang
- Shanghai Key Laboratory of Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
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208
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Ahmadi H, Ahmadi A, Azimzadeh-Jamalkandi S, Shoorehdeli MA, Salehzadeh-Yazdi A, Bidkhori G, Masoudi-Nejad A. HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens. Genomics 2012; 101:94-100. [PMID: 23174671 DOI: 10.1016/j.ygeno.2012.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 09/25/2012] [Accepted: 11/09/2012] [Indexed: 12/19/2022]
Abstract
MiRNAs play an essential role in the networks of gene regulation by inhibiting the translation of target mRNAs. Several computational approaches have been proposed for the prediction of miRNA target-genes. Reports reveal a large fraction of under-predicted or falsely predicted target genes. Thus, there is an imperative need to develop a computational method by which the target mRNAs of existing miRNAs can be correctly identified. In this study, combined pattern recognition neural network (PRNN) and principle component analysis (PCA) architecture has been proposed in order to model the complicated relationship between miRNAs and their target mRNAs in humans. The results of several types of intelligent classifiers and our proposed model were compared, showing that our algorithm outperformed them with higher sensitivity and specificity. Using the recent release of the mirBase database to find potential targets of miRNAs, this model incorporated twelve structural, thermodynamic and positional features of miRNA:mRNA binding sites to select target candidates.
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Affiliation(s)
- Hamed Ahmadi
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Ahmadi
- Department of Electrical and Computer Engineering, Khajeh-Nasir Toosi University, Tehran, Iran
| | - Sadegh Azimzadeh-Jamalkandi
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Salehzadeh-Yazdi
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Gholamreza Bidkhori
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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209
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Antiangiogenic role of miR-361 in human umbilical vein endothelial cells: functional interaction with the peptide somatostatin. Naunyn Schmiedebergs Arch Pharmacol 2012; 386:15-27. [PMID: 23128854 DOI: 10.1007/s00210-012-0808-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/22/2012] [Indexed: 12/15/2022]
Abstract
Somatostatin (SRIF) acts as antiangiogenic factor, but its role in the regulation of microRNAs (miRNAs) targeting proangiogenic factors is unknown. We used human umbilical vein endothelial cells (HUVEC) to investigate whether (1) miRNAs targeting proangiogenic factors are influenced by hypoxia, (2) their expression is regulated by SRIF, and (3) SRIF-regulated miRNAs affect HUVEC angiogenic phenotype. The involvement of signal transducer and activator of transcription (STAT) 3 and hypoxia inducible factor (HIF)-1 in miRNA effects was studied. Quantitative real-time PCR, Western blot, cell proliferation assays, and enzyme-linked immunosorbent assay (ELISA) were used. Using specific algorithms, three miRNAs (miR-17, miR-18b, and miR-361) were predicted to bind angiogenesis-associated factors including STAT3, HIF-1α, and vascular endothelial growth factor (VEGF). Hypoxia downregulates miR-17 and miR-361 without affecting miR-18b. SRIF restored decreased levels of miR-361 acting at the SRIF receptor sst(1). Downregulated miR-361 was also restored by HIF-1α inhibition with YC-1. Combined application of SRIF did not influence YC-1-induced miR-361 downregulation, suggesting that YC-1 and SRIF modulate miR-361 through a common mechanism involving HIF-1α. This possibility was confirmed by the result that HIF-1α activation in normoxia-downregulated miR-361 and that this downregulation was prevented by SRIF. miR-361 overexpression reduced hypoxia-induced cell proliferation and VEGF release indicating miR-361 involvement in the acquisition of an angiogenic phenotype by HUVEC. miR-361 effects on VEGF were enhanced by the coadministration of SRIF. Our results suggest that (1) SRIF regulates miR-361 expression through a control on HIF-1, (2) miR-361 affects HUVEC angiogenic phenotype, and (3) SRIF and miR-361 act cooperatively in limiting hypoxia-induced VEGF release.
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210
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Lee ST, Chu K, Jung KH, Kim JH, Huh JY, Yoon H, Park DK, Lim JY, Kim JM, Jeon D, Ryu H, Lee SK, Kim M, Roh JK. miR-206 regulates brain-derived neurotrophic factor in Alzheimer disease model. Ann Neurol 2012; 72:269-77. [PMID: 22926857 DOI: 10.1002/ana.23588] [Citation(s) in RCA: 248] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Alzheimer disease (AD) brains are deficient in brain-derived neurotrophic factor (BDNF), which regulates synaptic plasticity and memory. MicroRNAs (miRNAs) are ∼22-nucleotide small noncoding RNAs that control a variety of physiological and disease processes. Here, we show that miR-206 regulates BDNF and memory function in AD mice. METHODS Expression of miRNAs was analyzed in Tg2576 AD transgenic mice and human AD brain samples. Regulation of BDNF by a selected miRNA was validated by in silico prediction, target gene luciferase assay, and dendritic spine responses in neurons. AM206, a neutralizing inhibitor of miR-206 (antagomir), was injected into the third ventricle of Tg2576 mice, after which memory function, synaptogenesis, neurogenesis, and target gene expression were assessed. For noninvasive delivery, antagomirs were administered intranasally. RESULTS The brains of Tg2576 mice and the temporal cortex of human AD brains had increased levels of miR-206. This miRNA targeted BDNF transcripts, and AM206 prevented the detrimental effects of amyloid-β42 on BDNF and dendritic spine degeneration in Tg2576 neurons. Injection of AM206 into the cerebral ventricles of AD mice increased the brain levels of BDNF and improved their memory function. In parallel, AM206 enhanced the hippocampal synaptic density and neurogenesis. Furthermore, intranasally administered AM206 also reached the brain and increased BDNF levels and memory function in AD mice. INTERPRETATION Our findings demonstrate a novel miRNA-dependent regulation of BDNF in AD and suggest possible therapeutic approaches, such as noninvasive intranasal delivery of AM206.
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Affiliation(s)
- Soon-Tae Lee
- Department of Neurology, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
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211
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One decade of development and evolution of microRNA target prediction algorithms. GENOMICS PROTEOMICS & BIOINFORMATICS 2012. [PMID: 23200135 PMCID: PMC5054202 DOI: 10.1016/j.gpb.2012.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Nearly two decades have passed since the publication of the first study reporting the discovery of microRNAs (miRNAs). The key role of miRNAs in post-transcriptional gene regulation led to the performance of an increasing number of studies focusing on origins, mechanisms of action and functionality of miRNAs. In order to associate each miRNA to a specific functionality it is essential to unveil the rules that govern miRNA action. Despite the fact that there has been significant improvement exposing structural characteristics of the miRNA–mRNA interaction, the entire physical mechanism is not yet fully understood. In this respect, the development of computational algorithms for miRNA target prediction becomes increasingly important. This manuscript summarizes the research done on miRNA target prediction. It describes the experimental data currently available and used in the field and presents three lines of computational approaches for target prediction. Finally, the authors put forward a number of considerations regarding current challenges and future directions.
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212
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Abstract
Mutations of the neurofibromin 1 gene cause neurofibromatosis type 1, a disease in which learning and behavioral abnormalities are common. The disease is completely penetrant but shows variable phenotypic expression in patients. The repertoire of regulatory interactions utilized by neurons to control neurofibromin 1 expression is poorly understood. Here, we examined the contribution of microRNAs into this regulatory network. Using reporter assays, we provided evidence that miR-128 and to a lesser extent miR-137 and miR-103 reduced neurofibromin 1 reporter levels through specific binding to Nf1 3'-UTR. Mutations in all three predicted binding sites eliminated the reporter response. MiR-128 and miR-137, unlike miR-103 that showed a more ubiquitous expression, were predominantly expressed in brain with a distribution that resembled neurofibromin 1 expression in different tissues as well as during the course of neuronal development. In the nervous system, all three microRNAs showed highest expression in neurons and least in Schwann cells and astrocytes. Overexpression of miR-128 alone or with miR-103 and miR-137 significantly reduced endogenous neurofibromin 1 protein levels, while antisense inhibition of these microRNAs enhanced translation of endogenous neurofibromin 1 and reporter in primary cultures of hippocampal neurons. These findings revealed a significant additional mechanism by which neurofibromin 1 is regulated in neurons and implicated new candidates for the treatment of multifarious neurofibromatosis type 1 cognitive symptoms.
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Affiliation(s)
- Maria Paschou
- Molecular and Cellular Neurobiology Lab, Center of Neurosciences and Social Psychiatry, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Epaminondas Doxakis
- Molecular and Cellular Neurobiology Lab, Center of Neurosciences and Social Psychiatry, Biomedical Research Foundation, Academy of Athens, Athens, Greece
- * E-mail:
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213
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Vejnar CE, Zdobnov EM. MiRmap: comprehensive prediction of microRNA target repression strength. Nucleic Acids Res 2012; 40:11673-83. [PMID: 23034802 PMCID: PMC3526310 DOI: 10.1093/nar/gks901] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs, or miRNAs, post-transcriptionally repress the expression of protein-coding genes. The human genome encodes over 1000 miRNA genes that collectively target the majority of messenger RNAs (mRNAs). Base pairing of the so-called miRNA ‘seed’ region with mRNAs identifies many thousands of putative targets. Evaluating the strength of the resulting mRNA repression remains challenging, but is essential for a biologically informative ranking of potential miRNA targets. To address these challenges, predictors may use thermodynamic, evolutionary, probabilistic or sequence-based features. We developed an open-source software library, miRmap, which for the first time comprehensively covers all four approaches using 11 predictor features, 3 of which are novel. This allowed us to examine feature correlations and to compare their predictive power in an unbiased way using high-throughput experimental data from immunopurification, transcriptomics, proteomics and polysome fractionation experiments. Overall, target site accessibility appears to be the most predictive feature. Our novel feature based on PhyloP, which evaluates the significance of negative selection, is the best performing predictor in the evolutionary category. We combined all the features into an integrated model that almost doubles the predictive power of TargetScan. miRmap is freely available from http://cegg.unige.ch/mirmap.
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Affiliation(s)
- Charles E Vejnar
- Department of Genetic Medicine and Development, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
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214
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Dippold RP, Vadigepalli R, Gonye GE, Hoek JB. Chronic ethanol feeding enhances miR-21 induction during liver regeneration while inhibiting proliferation in rats. Am J Physiol Gastrointest Liver Physiol 2012; 303:G733-43. [PMID: 22790595 PMCID: PMC3468539 DOI: 10.1152/ajpgi.00019.2012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Liver regeneration is an important repair response to liver injury. Chronic ethanol consumption inhibits and delays liver regeneration in experimental animals. We studied the effects of chronic ethanol treatment on messenger RNA (mRNA) and microRNA (miRNA) expression profiles during the first 24 h after two-thirds partial hepatectomy (PHx) and found an increase in hepatic miR-21 expression in both ethanol-fed and pair-fed control rats after PHx. We demonstrate that the increase of miR-21 expression during liver regeneration is more robust in ethanol-fed rats. Peak miR-21 expression occurs at 24 h after PHx in both ethanol-fed and control rats, corresponding to the peak of hepatocyte S phase in control rats, but not in ethanol-exposed livers in which cell cycle is delayed. The induction of miR-21 24 h after PHx in control rats is not greater than the increase in expression of miR-21 due to sham surgery. However, in the ethanol-fed rat, miR-21 is induced to a greater extent by PHx than by sham surgery. To elucidate the implications of increased miR-21 expression during liver regeneration, we employed unbiased global target analysis using gene expression data compiled by our group. Our analyses suggest that miR-21 may play a greater role in regulating gene expression during regeneration in the ethanol-fed rat than in the control rat. Our analysis of potential targets of miR-21 suggests that miR-21 affects a broad range of target processes and may have a widespread regulatory role under conditions of suppressed liver regeneration in ethanol-treated animals.
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Affiliation(s)
- Rachael P. Dippold
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Gregory E. Gonye
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jan B. Hoek
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
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215
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Leone V, D'Angelo D, Pallante P, Croce CM, Fusco A. Thyrotropin regulates thyroid cell proliferation by up-regulating miR-23b and miR-29b that target SMAD3. J Clin Endocrinol Metab 2012; 97:3292-301. [PMID: 22730517 DOI: 10.1210/jc.2012-1349] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT MicroRNA (miRNA or miR) have emerged as an important class of short endogenous RNA that act as post-transcriptional regulators of gene expression and have a critical role in cell proliferation and differentiation. OBJECTIVES The aim of this study was to elucidate the role of miRNA in the proliferation of differentiated thyroid cells that require TSH for their growth. DESIGN To elucidate the role of miRNA in thyroid cell proliferation, we have analyzed the miRNA expression profile of PC Cl 3 cells before and after the stimulation by TSH. RESULTS We report the identification of two specific miRNA (miR-23b and miR-29b) whose up-regulation by TSH is required for thyroid cell growth. We identified mothers against decapentaplegic homolog 3 (Smad3), a member of the TGF-β pathway that has an inhibitor role in thyroid follicular cell proliferation as a target of miR-23b and miR-29b. Functional studies demonstrated that the overexpression of miR-23b and miR-29b promotes thyroid cell growth. Interestingly, an increased expression of both these miRNA was also detected in experimental and human goiters. CONCLUSIONS These findings support the idea that the regulation of miRNA expression synergizes with the traditional proliferation pathways in promoting cell growth.
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Affiliation(s)
- Vincenza Leone
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR (Consiglio Nazionale delle Ricerche), Dipartimento di Biologia e Patologia Cellulare e Molecolare, Facoltà di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli Federico II 80131 Naples, Italy
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216
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Oulas A, Karathanasis N, Louloupi A, Iliopoulos I, Kalantidis K, Poirazi P. A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2. RNA Biol 2012; 9:1196-207. [PMID: 22954617 DOI: 10.4161/rna.21725] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Computational methods for miRNA target prediction vary in the algorithm used; and while one can state opinions about the strengths or weaknesses of each particular algorithm, the fact of the matter is that they fall substantially short of capturing the full detail of physical, temporal and spatial requirements of miRNA::target-mRNA interactions. Here, we introduce a novel miRNA target prediction tool called Targetprofiler that utilizes a probabilistic learning algorithm in the form of a hidden Markov model trained on experimentally verified miRNA targets. Using a large scale protein downregulation data set we validate our method and compare its performance to existing tools. We find that Targetprofiler exhibits greater correlation between computational predictions and protein downregulation and predicts experimentally verified miRNA targets more accurately than three other tools. Concurrently, we use primer extension to identify the mature sequence of a novel miRNA gene recently identified within a cancer associated genomic region and use Targetprofiler to predict its potential targets. Experimental verification of the ability of this small RNA molecule to regulate the expression of CCND2, a gene with documented oncogenic activity, confirms its functional role as a miRNA. These findings highlight the competitive advantage of our tool and its efficacy in extracting biologically significant results.
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Affiliation(s)
- Anastasis Oulas
- Institute of Molecular Biology and Biotechnology-FORTH, Heraklion, Crete, Greece
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217
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Bauer KM, Hummon AB. Effects of the miR-143/-145 microRNA cluster on the colon cancer proteome and transcriptome. J Proteome Res 2012; 11:4744-54. [PMID: 22897626 DOI: 10.1021/pr300600r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The miR-143/-145 cluster is greatly reduced in several cancers, including colon cancer. Both miR-143 and miR-145 have been shown to possess antitumorigenic activity with involvement in various cancer-related events such as proliferation, invasion, and migration. As the deregulation of the miR-143/-145 cluster is implicated in tumorigenesis, we combined SILAC and microarray analyses to systematically interrogate the impact of miR-143/-145 on the colon cancer proteome and transcriptome. Using SILAC, we identified over 2000 proteins after reintroduction of miR-143 and miR-145, in the colon cancer cell line SW480, individually, and then, in concert. Our goal was to determine whether these microRNAs function individually or synergistically. The resulting regulated gene products showed evidence of both mRNA destabilization and translational inhibition with a bias toward the former mechanism of regulation. Numerous candidate targets were identified whose expression is attributable to an individual microRNA or whose regulation was more apparent following reintroduction of the miR-143/-145 cluster. In addition, several shared targets of miR-143 and miR-145 were identified. Overall, our results indicate that the summed effects of individually introduced microRNAs produce distinct molecular changes from the consequences of the assembled cluster. We conclude that there is a need to investigate both the individual and combined functional implications of a microRNA cluster.
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Affiliation(s)
- Kerry M Bauer
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
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218
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Wenzel A, Akbasli E, Gorodkin J. RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. ACTA ACUST UNITED AC 2012; 28:2738-46. [PMID: 22923300 PMCID: PMC3476332 DOI: 10.1093/bioinformatics/bts519] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Motivation: Regulatory, non-coding RNAs often function by forming a duplex with other RNAs. It is therefore of interest to predict putative RNA–RNA duplexes in silico on a genome-wide scale. Current computational methods for predicting these interactions range from fast complementary-based searches to those that take intramolecular binding into account. Together these methods constitute a trade-off between speed and accuracy, while leaving room for improvement within the context of genome-wide screens. A fast pre-filtering of putative duplexes would therefore be desirable. Results: We present RIsearch, an implementation of a simplified Turner energy model for fast computation of hybridization, which significantly reduces runtime while maintaining accuracy. Its time complexity for sequences of lengths m and n is with a much smaller pre-factor than other tools. We show that this energy model is an accurate approximation of the full energy model for near-complementary RNA–RNA duplexes. RIsearch uses a Smith–Waterman-like algorithm using a dinucleotide scoring matrix which approximates the Turner nearest-neighbor energies. We show in benchmarks that we achieve a speed improvement of at least 2.4× compared with RNAplex, the currently fastest method for searching near-complementary regions. RIsearch shows a prediction accuracy similar to RNAplex on two datasets of known bacterial short RNA (sRNA)–messenger RNA (mRNA) and eukaryotic microRNA (miRNA)–mRNA interactions. Using RIsearch as a pre-filter in genome-wide screens reduces the number of binding site candidates reported by miRNA target prediction programs, such as TargetScanS and miRanda, by up to 70%. Likewise, substantial filtering was performed on bacterial RNA–RNA interaction data. Availability: The source code for RIsearch is available at: http://rth.dk/resources/risearch. Contact:gorodkin@rth.dk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anne Wenzel
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark
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219
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Zhang X, Zeng J, Zhou M, Li B, Zhang Y, Huang T, Wang L, Jia J, Chen C. The tumor suppressive role of miRNA-370 by targeting FoxM1 in acute myeloid leukemia. Mol Cancer 2012; 11:56. [PMID: 22900969 PMCID: PMC3533721 DOI: 10.1186/1476-4598-11-56] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 08/06/2012] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Recent evidence has accumulated that MicroRNA (miRNA) dysregulation occurs in the majority of human malignancies including acute myeloid leukemia (AML) and may contribute to onco-/leukemo-genesis. METHODS The expression levels of miR-370 and FoxM1 were assessed in 48 newly diagnosed AML patients, 40 AML patients in 1st complete remission (CR) and 21 healthy controls. Quantitative real-time PCR, western blots, colony formation assay, and β-Galactosidase ( SA-β-Gal) staining were used to characterize the changes induced by overexpression or inhibition of miR-370 or FoxM1. RESULTS We found that the down-regulation of miR-370 expression was a frequent event in both leukemia cell lines and primary leukemic cells from patients with de novo AML. Lower levels of miR-370 expression were found in 37 of 48 leukemic samples from AML patients compared to those in bone marrow cells derived from healthy adult individuals. Ectopic expression of miR-370 in HL60 and K562 cells led to cell growth arrest and senescence. In contrast, depletion of miR-370 expression using RNA interference enhanced the proliferation of those leukemic cells. Mechanistically, miR-370 targets the transcription factor FoxM1, a well established oncogenic factor promoting cell cycle progression. Moreover, when HL60 and K562 cells were treated with 5-aza-2'-deoxycytidine, a DNA methylation inhibitor, miR-370 expression was up-regulated, which indicates epigenetic silencing of miR-370 in leukemic cells. CONCLUSIONS Taken together, miR-370 may function as a tumor suppressor by targeting FoxM1, and the epigenetic silence of miR-370 thus leads to derepression of FoxM1 expression and consequently contributes to AML development and progression.
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Affiliation(s)
- Xiaolu Zhang
- Department of Hematology, Qilu Hospital, Shandong University, No.107, Wenhua Xi Road, Jinan, 250012, Shandong, P. R. China
- Department of Medicine, Division of Hematology and CMM, Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden
| | - Jiping Zeng
- Department of Biochemistry, Shandong University, Jinan, China
| | - Minran Zhou
- Department of Hematology, Qilu Hospital, Shandong University, No.107, Wenhua Xi Road, Jinan, 250012, Shandong, P. R. China
| | - Bingnan Li
- Department of Microbiology/Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, China
- Department of Medicine, Division of Hematology and CMM, Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden
| | - Yuanyuan Zhang
- Department of Hematology, Qilu Hospital, Shandong University, No.107, Wenhua Xi Road, Jinan, 250012, Shandong, P. R. China
| | - Tao Huang
- Department of Hematology, Qilu Hospital, Shandong University, No.107, Wenhua Xi Road, Jinan, 250012, Shandong, P. R. China
- Department of Microbiology/Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, China
| | - Lixiang Wang
- Department of Microbiology/Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, China
| | - Jihui Jia
- Department of Microbiology/Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, China
| | - Chunyan Chen
- Department of Hematology, Qilu Hospital, Shandong University, No.107, Wenhua Xi Road, Jinan, 250012, Shandong, P. R. China
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Chen Z, Liang S, Zhao Y, Han Z. miR-92b regulates Mef2 levels through a negative-feedback circuit during Drosophila muscle development. Development 2012; 139:3543-52. [PMID: 22899845 DOI: 10.1242/dev.082719] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mef2 is the key transcription factor for muscle development and differentiation in Drosophila. It activates hundreds of downstream target genes, including itself. Precise control of Mef2 levels is essential for muscle development as different Mef2 protein levels activate distinct sets of muscle genes, but how this is achieved remains unclear. Here, we have identified a novel heart- and muscle-specific microRNA, miR-92b, which is activated by Mef2 and subsequently downregulates Mef2 through binding to its 3'UTR, forming a negative regulatory circuit that fine-tunes the level of Mef2. Deletion of miR-92b caused abnormally high Mef2 expression, leading to muscle defects and lethality. Blocking miR-92b function using microRNA sponge techniques also increased Mef2 levels and caused muscle defects similar to those seen with the miR-92b deletion. Additionally, overexpression of miR-92b reduced Mef2 levels and caused muscle defects similar to those seen in Mef2 RNAi, and Mef2 overexpression led to reversal of these defects. Our results suggest that the negative feedback circuit between miR-92b and Mef2 efficiently maintains the stable expression of both components that is required for homeostasis during Drosophila muscle development.
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Affiliation(s)
- Zhimin Chen
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan Medical School, 109 Zina Pitcher Place, 4029 BSRB, Ann Arbor, MI 48109, USA
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221
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Casanova-Salas I, Rubio-Briones J, Fernández-Serra A, López-Guerrero JA. miRNAs as biomarkers in prostate cancer. Clin Transl Oncol 2012; 14:803-11. [PMID: 22855165 DOI: 10.1007/s12094-012-0877-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 06/07/2012] [Indexed: 12/21/2022]
Abstract
Current prostate cancer (PCa) diagnosis is based in the serum prostate-specific antigen biomarker and digital rectal examination. However, these methods are limited by a low predictive value (24-37 %) and a high risk of mistaken results. During last years, new promising biomarkers such as Prostate Cancer Antigen 3 (PCA-3) and TMPRSS2-ETS fusion genes have been evaluated for their clinical use. However, the search of new biomarkers that could be used for PCa diagnosis and prognosis is still needed. Recent studies have demonstrated that the aberrant expression of microRNAs (miRNAs), small non-coding RNAs that negatively regulate gene expression, is related with the development of several cancers, including PCa. Since miRNAs serve as phenotypic signatures of different cancers, they appear as potential diagnostic, prognostic and therapeutic tools. Here, we review the current knowledge of miRNA expression patterns in PCa and their role in PCa prognosis and therapeutics.
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Affiliation(s)
- Irene Casanova-Salas
- Laboratory of Molecular Biology, Fundacion Instituto Valenciano de Oncologia, Profesor Beltran Baguena 8, 46009, Valencia, Spain
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222
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Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. BMC SYSTEMS BIOLOGY 2012; 6:90. [PMID: 22824421 PMCID: PMC3430561 DOI: 10.1186/1752-0509-6-90] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 07/09/2012] [Indexed: 12/31/2022]
Abstract
Background Transcription factors (TFs) have long been known to be principally activators of transcription in eukaryotes and prokaryotes. The growing awareness of the ubiquity of microRNAs (miRNAs) as suppressive regulators in eukaryotes, suggests the possibility of a mutual, preferential, self-regulatory connectivity between miRNAs and TFs. Here we investigate the connectivity from TFs and miRNAs to other genes and each other using text mining, TF promoter binding site and 6 different miRNA binding site prediction methods. Results In the first approach text mining of PubMed abstracts reveal statistically significant associations between miRNAs and both TFs and signal transduction gene classes. Secondly, prediction of miRNA targets in human and mouse 3’UTRs show enrichment only for TFs but not consistently across prediction methods for signal transduction or other gene classes. Furthermore, a random sample of 986 TarBase entries was scored for experimental evidence by manual inspection of the original papers, and enrichment for TFs was observed to increase with score. Low-scoring TarBase entries, where experimental evidence is anticorrelated miRNA:mRNA expression with predicted miRNA targets, appear not to select for real miRNA targets to any degree. Our manually validated text-mining results also suggests that miRNAs may be activated by more TFs than other classes of genes, as 7% of miRNA:TF co-occurrences in the literature were TFs activating miRNAs. This was confirmed when thirdly, we found enrichment for predicted, conserved TF binding sites in miRNA and TF genes compared to other gene classes. Conclusions We see enrichment of connections between miRNAs and TFs using several independent methods, suggestive of a network of mutual activating and suppressive regulation. We have also built regulatory networks (containing 2- and 3-loop motifs) for mouse and human using predicted miRNA and TF binding sites and we have developed a web server to search and display these loops, available for the community at http://rth.dk/resources/tfmirloop.
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223
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Lages E, Ipas H, Guttin A, Nesr H, Berger F, Issartel JP. MicroRNAs: molecular features and role in cancer. Front Biosci (Landmark Ed) 2012; 17:2508-40. [PMID: 22652795 DOI: 10.2741/4068] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
microRNAs (miRNAs) are small noncoding endogenously produced RNAs that play key roles in controlling the expression of many cellular proteins. Once they are recruited and incorporated into a ribonucleoprotein complex miRISC, they can target specific mRNAs in a miRNA sequence-dependent process and interfere in the translation into proteins of the targeted mRNAs via several mechanisms. Consequently, miRNAs can regulate many cellular pathways and processes. Dysregulation of their physiological roles may largely contribute to disease. In particular, in cancer, miRNAs can be involved in the deregulation of the expression of important genes that play key roles in tumorigenesis, tumor development, and angiogenesis and have oncogenic or tumor suppressor roles. This review focuses on the biogenesis and maturation of miRNAs, their mechanisms of gene regulation, and the way their expression is deregulated in cancer. The involvement of miRNAs in several oncogenic pathways such as angiogenesis and apoptosis, and in the inter-cellular dialog mediated by miRNA-loaded exosomes as well as the development of new therapeutical strategies based on miRNAs will be discussed.
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Affiliation(s)
- Elodie Lages
- INSERM, U836, Team7 Nanomedicine and Brain, BP 170, Grenoble, France
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224
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Landi D, Gemignani F, Landi S. Role of variations within microRNA-binding sites in cancer. Mutagenesis 2012; 27:205-10. [PMID: 22294768 DOI: 10.1093/mutage/ger055] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Over 2000 microRNA (miRNA) sequences from different species have been submitted to the miRBase, the central online repository for miRNAs, making a total of 5071 miRNA loci, expressing 5922 distinct mature miRNA sequences. In this review, we have addressed the importance of the genetic variations in humans affecting miRNAs, their target genes and the genes involved in miRNA processing for individual risk of cancer, with particular emphasis on colorectal cancer. In fact, the number of studies suggesting that individual predisposition to cancer is modulated by genetic polymorphisms affecting the biogenesis of miRNA and the interaction between miRNAs and targets has risen steeply in the last few years. We also report the first evidence that variant alleles of single-nucleotide polymorphisms (SNPs) within miRNA genes and miRNA targets, previously associated with the risk of cancer, behave differently when tested in functional studies. The SNPs belonging to the miRNA world are certainly contributing to new insights in the field of the genetic predisposition to disease.
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Affiliation(s)
- Debora Landi
- Department of Biology, University of Pisa, Via Derna 1, 56100 Pisa, Italy
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225
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Zeng L, Childs SJ. The smooth muscle microRNA miR-145 regulates gut epithelial development via a paracrine mechanism. Dev Biol 2012; 367:178-86. [PMID: 22609551 DOI: 10.1016/j.ydbio.2012.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 04/27/2012] [Accepted: 05/03/2012] [Indexed: 01/25/2023]
Abstract
MicroRNAs are potent modulators of cellular differentiation. miR-145 is expressed in, and promotes the differentiation of vascular and visceral smooth muscle cells (SMCs). Interestingly, we have observed that miR-145 also promotes differentiation of the gut epithelium in the developing zebrafish, a cell type where it is not expressed. Here we identify that a paracrine pathway involving the morphogens Sonic hedgehog (Shh) in epithelium and bone morphogenic protein 4 (Bmp4) in SMCs is modulated by miR-145. We show that expression of miR-145 in visceral SMCs normally represses the expression of the morphogen bmp4, as loss of miR-145 leads to upregulation of bmp4 in SMCs. We show that bmp4 in turn controls expression of Shh in the visceral epithelium. Conversely, in miR-145 morphants where bmp4 expression is increased, expression of sonic hedgehog a (shha) is strongly increased in gut epithelium. We show that expression of bmp4 is modulated by the miR-145 direct target gata6 but not a second potential direct target, klf5a. Thus although miR-145 is a tissue-restricted microRNA, it plays an essential role in promoting the patterning of both gut layers during gut development via a paracrine mechanism.
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Affiliation(s)
- Lei Zeng
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada T2N 4N1
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226
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Cao S, Chen SJ. Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity. Nucleic Acids Res 2012; 40:4681-90. [PMID: 22307238 PMCID: PMC3378890 DOI: 10.1093/nar/gks052] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of short RNA molecules that play an important role in post-transcriptional gene regulation. Computational prediction of the miRNA target sites in mRNA is crucial for understanding the mechanism of miRNA-mRNA interactions. We here develop a new computational model that allows us to treat a variety of miRNA-mRNA kissing interactions, which have been ignored in the currently existing miRNA target prediction algorithms. By including all the different inter- and intra-molecular base pairs, this new model can predict both the structural accessibility of the target sites and the binding affinity (free energy). Applications of the model to a test set of 105 miRNA-gene systems show a notably improved success rate of 83/105. We found that although the binding affinity alone predicts the miRNA repression efficiency with a high success rate of 73/105, the structure in the seed region can significantly influence the miRNA activity. The method also allows us to efficiently search for the potent miRNA from a pool of miRNA candidates for any given gene target. Furthermore, extension of the method may enable predictions of the three-dimensional (3D) structures of miRNA/mRNA complexes.
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Affiliation(s)
- Song Cao
- Department of Physics, University of Missouri, Columbia, MO 65211, USA
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227
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Tachibana A, Yamada Y, Ida H, Saito S, Tanabe T. LidNA, a novel miRNA inhibitor constructed with unmodified DNA. FEBS Lett 2012; 586:1529-32. [PMID: 22673521 DOI: 10.1016/j.febslet.2012.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/21/2012] [Accepted: 04/11/2012] [Indexed: 02/07/2023]
Abstract
Many miRNA inhibitors have been developed and they are chemically modified oligonucleotides such as 2?-O-methylated RNA and locked nucleic acid (LNA). Unmodified DNA was not yet reported as a miRNA inhibitor because of the low affinity of DNA/miRNA compared to mRNA/miRNA. We designed a structured unmodified DNA that significantly inhibits miRNA function. The clue structure for activity is the miRNA binding site between double stranded regions which is responsible for the miRNA inhibitory activity and tight binding to miRNA. We developed the miRNA inhibitor constructed with unmodified DNA, and named it LidNA, DNA that puts a lid on miRNA function.
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Affiliation(s)
- Akira Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, Sumiyoshi-ku, Osaka, Japan.
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228
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Li Z, Cao Y, Jie Z, Liu Y, Li Y, Li J, Zhu G, Liu Z, Tu Y, Peng G, Lee DW, Park SS. miR-495 and miR-551a inhibit the migration and invasion of human gastric cancer cells by directly interacting with PRL-3. Cancer Lett 2012; 323:41-47. [PMID: 22469786 DOI: 10.1016/j.canlet.2012.03.029] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 03/04/2012] [Accepted: 03/26/2012] [Indexed: 12/19/2022]
Abstract
The phosphatase of regenerating liver-3 (PRL-3) gene is associated with metastasis in gastric cancer, and is believed to play a causative role by promoting tumor cell motility, invasion, and metastasis, but little is known of the mechanisms involved. We previously reported that PRL-3 expression is significantly higher in the tissues of primary gastric carcinomas with peritoneal metastasis. In the present study, we found that two microRNAs (miRNAs), miR-495 and miR-551a, predicted to target PRL-3, are downregulated in gastric carcinoma samples. The validation of this interaction between those two miRNAs and PRL-3 was confirmed by western blotting and quantitative real-time PCR (qPCR) in GC cell lines transfected with miR-495 and miR-551a mimics. Furthermore, the migration and invasion of GC cells were significantly inhibited by transfection with miR-495 or -551a mimics, and the mRNA and protein levels of PRL-3 were reduced in cells overexpressing miR-495 or -551a. Collectively, our findings suggest that miR-495 and miR-551a both act as tumor suppressors by targeting the PRL-3 oncogene and inhibiting gastric cancer cell migration and invasion. The findings of this study contribute to current understanding of the functions of miRNA mimics in GC gene therapy.
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Affiliation(s)
- Zhengrong Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China.
| | - Yi Cao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Zhigang Jie
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China.
| | - Yi Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yingliang Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Junhe Li
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Guoming Zhu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Zhengren Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yi Tu
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Gen Peng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Dong-Woo Lee
- Department of Surgery, Korea University Anam Hospital, South Korea
| | - Sung-Soo Park
- Department of Surgery, Korea University Anam Hospital, South Korea
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Menabò S, Balsamo A, Baldazzi L, Barbaro M, Nicoletti A, Conti V, Pirazzoli P, Wedell A, Cicognani A. A sequence variation in 3'UTR of CYP21A2 gene correlates with a mild form of congenital adrenal hyperplasia. J Endocrinol Invest 2012; 35:298-305. [PMID: 21521936 DOI: 10.3275/7680] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Congenital adrenal hyperplasia (CAH) is mainly caused by the deficiency of the 21-hydroxylase enzyme coded by the CYP21A2 gene. However, some alleles in the non-classical form (NC-CAH) remain without identified mutations, suggesting the involvement of regulatory regions. AIM Our objective was to study an allele carrying the variant *13 G>A in the 3'UTR of the CYP21A2 gene identified in some patients with a mild form of NC-CAH in order to verify the possible implication of this variation with the phenotype observed. SUBJECTS AND METHODS Among all the subjects in whom the CYP21A2 gene was analyzed, 14 patients and 7 relatives heterozygous or homozygous for the *13 G>A substitution in 3'UTR were selected. Sequencing of DNA, genotyping, multiplex ligation-dependent probe amplification (MLPA), in vitro studies and bioinformatic analysis were performed. RESULTS The haplotype of the *13 G>A allele was identical in all the subjects with a monomodular structure composed by one C4A gene and one CYP21A2 gene without a second module with the CYP21A1P pseudogene. No other concomitant mutations were found in the region extending from 3 kb in the promoter and encompassing the polyadenylation signal. Both bioinformatic analysis and in vitro studies predicted an alteration of the RNA folding and expression, but no miRNA target sequences were found in this region. CONCLUSIONS The identification of a substitution in the 3'UTR of the gene associated with a mild form of NC-CAH suggests the importance of analyzing the CYP21A2 untranslated regions to better characterize and treat this subgroup of patients.
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Affiliation(s)
- S Menabò
- Department of Gynaecologic, Obstetric, and Paediatric Sciences, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
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230
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Teo MT, Landi D, Taylor CF, Elliott F, Vaslin L, Cox DG, Hall J, Landi S, Bishop D, Kiltie AE. The role of microRNA-binding site polymorphisms in DNA repair genes as risk factors for bladder cancer and breast cancer and their impact on radiotherapy outcomes. Carcinogenesis 2012; 33:581-6. [PMID: 22166496 PMCID: PMC3291859 DOI: 10.1093/carcin/bgr300] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 11/18/2011] [Accepted: 12/07/2011] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in post-transcriptional regulation of gene expression through binding to messenger RNAs (mRNA) thereby promoting mRNA degradation or altered translation. A single-nucleotide polymorphism (SNP) located within a miRNA-binding site could thus alter mRNA translation and influence cancer risk and treatment response. The common SNPs located within the 3'-untranslated regions of 20 DNA repair genes were analysed for putative miRNA-binding sites using bioinformatics algorithms, calculating the difference in Gibbs free binding energy (ΔΔG) for each wild-type versus variant allele. Seven SNPs were selected to be genotyped in germ line DNAs both from a bladder cancer case-control series (752 cases and 704 controls) and 202 muscle-invasive bladder cancer radiotherapy cases. The PARP-1 SNP rs8679 was also genotyped in a breast cancer case-control series (257 cases and 512 controls). Without adjustment for multiple testing, multivariate analysis demonstrated an association with increased bladder cancer risk with PARP1 rs8679 (P(trend) = 0.05) while variant homozygotes of PARP1 rs8679 were also noted to have an increased breast cancer risk (P = 0.03). In the radiotherapy cases, carriers of the RAD51 rs7180135 minor allele had improved cancer-specific survival (hazard ratio 0.52, 95% confidence interval 0.31-0.87, P = 0.01). This is the first report of associations between DNA repair gene miRNA-binding site SNPs with bladder and breast cancer risk and radiotherapy outcomes. If validated, these findings may give further insight into the biology of bladder carcinogenesis, allow testing of the RAD51 SNP as a potential predictive biomarker and also reveal potential targets for new cancer treatments.
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Affiliation(s)
| | - Debora Landi
- Dipartimento di Biologia, University of Pisa, Pisa 56126, Italy
| | | | | | - Laurence Vaslin
- INSERM U612, Orsay 91405, France
- Institut Curie, Orsay 91405, France
| | - David G. Cox
- Lyon Cancer Research Centre, INSERM U1052, Lyon 69008, France
| | - Janet Hall
- INSERM U612, Orsay 91405, France
- Institut Curie, Orsay 91405, France
| | - Stefano Landi
- Dipartimento di Biologia, University of Pisa, Pisa 56126, Italy
| | | | - Anne E. Kiltie
- Department of Oncology, Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford OX3 7DU, UK
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Three Drosophila Hox complex microRNAs do not have major effects on expression of evolutionarily conserved Hox gene targets during embryogenesis. PLoS One 2012; 7:e31365. [PMID: 22393361 PMCID: PMC3290615 DOI: 10.1371/journal.pone.0031365] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 01/09/2012] [Indexed: 12/21/2022] Open
Abstract
The discovery of microRNAs has resulted in a major expansion of the number of molecules known to be involved in gene regulation. Elucidating the functions of animal microRNAs has posed a significant challenge as their target interactions with messenger RNAs do not adhere to simple rules. Of the thousands of known animal microRNAs, relatively few microRNA:messenger RNA regulatory interactions have been biologically validated in an normal organismal context. Here we present evidence that three microRNAs from the Hox complex in Drosophila (miR-10-5p, miR-10-3p, miR-iab-4-5p) do not have significant effects during embryogenesis on the expression of Hox genes that contain high confidence microRNAs target sites in the 3′ untranslated regions of their messenger RNAs. This is significant, in that it suggests that many predicted microRNA-target interactions may not be biologically relevant, or that the outcomes of these interactions may be so subtle that mutants may only show phenotypes in specific contexts, such as in environmental stress conditions, or in combinations with other microRNA mutations.
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232
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Honda N, Jinnin M, Kajihara I, Makino T, Makino K, Masuguchi S, Fukushima S, Okamoto Y, Hasegawa M, Fujimoto M, Ihn H. TGF-β-mediated downregulation of microRNA-196a contributes to the constitutive upregulated type I collagen expression in scleroderma dermal fibroblasts. THE JOURNAL OF IMMUNOLOGY 2012; 188:3323-31. [PMID: 22379029 DOI: 10.4049/jimmunol.1100876] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Previous reports indicated the significance of the TGF-β signaling in the pathogenesis of systemic sclerosis. We tried to evaluate the possibility that microRNAs (miRNAs) play a part in the type I collagen upregulation seen in normal fibroblasts stimulated with exogenous TGF-β and systemic sclerosis (SSc) fibroblasts. miRNA expression profile was evaluated by miRNA PCR array and real-time PCR. The protein expression of type I collagen was determined by immunoblotting. In vivo detection of miRNA in paraffin section was performed by in situ hybridization. Several miRNAs were found to be downregulated in both TGF-β-stimulated normal fibroblasts and SSc fibroblasts compared with normal fibroblasts by PCR array. Among them, miR-196a expression was decreased in SSc both in vivo and in vitro by real-time PCR or in situ hybridization. In SSc fibroblasts, miR-196a expression was normalized by TGF-β small interfering RNA. miR-196a inhibitor leads to the overexpression of type I collagen in normal fibroblasts, whereas overexpression of the miRNA resulted in the downregulation of type I collagen in SSc fibroblasts. In addition, miR-196a was detectable and quantitative in the serum of SSc patients. Patients with lower serum miR-196a levels had significantly higher ratio of diffuse cutaneous SSc:limited cutaneous SSc, higher modified Rodnan total skin thickness score, and higher prevalence of pitting scars than those without. miR-196a may play some roles in the pathogenesis of SSc. Investigation of the regulatory mechanisms of type I collagen expression by miR-196a may lead to new treatments using miRNA.
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Affiliation(s)
- Noritoshi Honda
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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233
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Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses. Sci Rep 2012; 2:282. [PMID: 22355792 PMCID: PMC3282946 DOI: 10.1038/srep00282] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 01/31/2012] [Indexed: 12/31/2022] Open
Abstract
The use of small molecules to target miRNAs is a new type of therapy for human diseases, particularly cancers. We proposed a novel high-throughput approach to identify the biological links between small molecules and miRNAs in 23 different cancers and constructed the Small Molecule-MiRNA Network (SMirN) for each cancer to systematically analyze the properties of their associations. In each SMirN, we partitioned small molecules (miRNAs) into modules, in which small molecules (miRNAs) were connected with one miRNA (small molecule). Almost all of the miRNA modules comprised miRNAs that had similar target genes and functions or were members of the same miRNA family. Most of the small molecule modules involved compounds with similar chemical structures, modes of action, or drug interactions. These modules can be used to identify drug candidates and new indications for existing drugs. Therefore, our approach is valuable to drug discovery and cancer therapy.
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234
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Tan GS, Chiu CH, Garchow BG, Metzler D, Diamond SL, Kiriakidou M. Small molecule inhibition of RISC loading. ACS Chem Biol 2012; 7:403-10. [PMID: 22026461 PMCID: PMC3282558 DOI: 10.1021/cb200253h] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Argonaute proteins are the core components of the microRNP/RISC.
The biogenesis and function of microRNAs and endo- and exo- siRNAs
are regulated by Ago2, an Argonaute protein with RNA binding and nuclease
activities. Currently, there are no in vitro assays
suitable for large-scale screening of microRNP/RISC loading modulators.
We describe a novel in vitro assay that is based
on fluorescence polarization of TAMRA-labeled RNAs loaded to human
Ago2. Using this assay, we identified potent small-molecule inhibitors
of RISC loading, including aurintricarboxylic acid (IC50 = 0.47 μM), suramin (IC50 = 0.69 μM), and
oxidopamine HCL (IC50 = 1.61 μM). Small molecules
identified by this biochemical screening assay also inhibited siRNA
loading to endogenous Ago2 in cultured cells.
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Affiliation(s)
- Grace S. Tan
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Chun-Hao Chiu
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Barry G. Garchow
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - David Metzler
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Scott L. Diamond
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Marianthi Kiriakidou
- Department
of Medicine and ‡Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
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235
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Chen C, Deng B, Qiao M, Zheng R, Chai J, Ding Y, Peng J, Jiang S. Solexa sequencing identification of conserved and novel microRNAs in backfat of Large White and Chinese Meishan pigs. PLoS One 2012; 7:e31426. [PMID: 22355364 PMCID: PMC3280305 DOI: 10.1371/journal.pone.0031426] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 01/08/2012] [Indexed: 01/08/2023] Open
Abstract
The domestic pig (Sus scrofa), an important species in animal production industry, is a right model for studying adipogenesis and fat deposition. In order to expand the repertoire of porcine miRNAs and further explore potential regulatory miRNAs which have influence on adipogenesis, high-throughput Solexa sequencing approach was adopted to identify miRNAs in backfat of Large White (lean type pig) and Meishan pigs (Chinese indigenous fatty pig). We identified 215 unique miRNAs comprising 75 known pre-miRNAs, of which 49 miRNA*s were first identified in our study, 73 miRNAs were overlapped in both libraries, and 140 were novelly predicted miRNAs, and 215 unique miRNAs were collectively corresponding to 235 independent genomic loci. Furthermore, we analyzed the sequence variations, seed edits and phylogenetic development of the miRNAs. 17 miRNAs were widely conserved from vertebrates to invertebrates, suggesting that these miRNAs may serve as potential evolutional biomarkers. 9 conserved miRNAs with significantly differential expressions were determined. The expression of miR-215, miR-135, miR-224 and miR-146b was higher in Large White pigs, opposite to the patterns shown by miR-1a, miR-133a, miR-122, miR-204 and miR-183. Almost all novel miRNAs could be considered pig-specific except ssc-miR-1343, miR-2320, miR-2326, miR-2411 and miR-2483 which had homologs in Bos taurus, among which ssc-miR-1343, miR-2320, miR-2411 and miR-2483 were validated in backfat tissue by stem-loop qPCR. Our results displayed a high level of concordance between the qPCR and Solexa sequencing method in 9 of 10 miRNAs comparisons except for miR-1a. Moreover, we found 2 miRNAs, miR-135 and miR-183, may exert impacts on porcine backfat development through WNT signaling pathway. In conclusion, our research develops porcine miRNAs and should be beneficial to study the adipogenesis and fat deposition of different pig breeds based on miRNAs.
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Affiliation(s)
- Chen Chen
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Bing Deng
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Mu Qiao
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Rong Zheng
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jin Chai
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yi Ding
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jian Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
- * E-mail: (SJ); (JP)
| | - Siwen Jiang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
- * E-mail: (SJ); (JP)
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236
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Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG. Functional microRNA targets in protein coding sequences. ACTA ACUST UNITED AC 2012; 28:771-6. [PMID: 22285563 DOI: 10.1093/bioinformatics/bts043] [Citation(s) in RCA: 378] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
MOTIVATION Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression. RESULTS Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data. The analysis is performed independently for the CDS and the 3(')-untranslated regions (3(')-UTRs) and reveals different sets of features and models for the two regions. The two models are combined into a novel computational model for miRNA target genes, DIANA-microT-CDS, which achieves higher sensitivity compared with other popular programs and the model that uses only the 3(')-UTR target sites. Further analysis indicates that genes with shorter 3(')-UTRs are preferentially targeted in the CDS, suggesting that evolutionary selection might favor additional sites on the CDS in cases where there is restricted space on the 3(')-UTR.
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Affiliation(s)
- Martin Reczko
- Institute of Molecular Oncology, Biomedical Sciences Research Center, Vari, Greece.
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237
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Heller G, Weinzierl M, Noll C, Babinsky V, Ziegler B, Altenberger C, Minichsdorfer C, Lang G, Döme B, End-Pfützenreuter A, Arns BM, Grin Y, Klepetko W, Zielinski CC, Zöchbauer-Müller S. Genome-Wide miRNA Expression Profiling Identifies miR-9-3 and miR-193a as Targets for DNA Methylation in Non–Small Cell Lung Cancers. Clin Cancer Res 2012; 18:1619-29. [DOI: 10.1158/1078-0432.ccr-11-2450] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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238
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Landi D, Gemignani F, Pardini B, Naccarati A, Garritano S, Vodicka P, Vodickova L, Canzian F, Novotny J, Barale R, Landi S. Identification of candidate genes carrying polymorphisms associated with the risk of colorectal cancer by analyzing the colorectal mutome and microRNAome. Cancer 2012; 118:4670-80. [PMID: 22282400 DOI: 10.1002/cncr.27435] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 10/31/2011] [Accepted: 11/18/2011] [Indexed: 12/16/2022]
Abstract
BACKGROUND The presence of single-nucleotide polymorphisms (SNPs) within the 3'-untranslated regions of genes could affect the binding between a microRNA (miRNA) and its target, with consequences on gene expression regulation. Considering the important role of miRNAs in carcinogenesis, it is hypothesized here that these SNPs could also affect the individual risk of colorectal cancer (CRC). METHODS To test this hypothesis, a list was developed of 140 somatically mutated genes deduced from previous works on the mutome of the CRC. A further selection was conducted of SNPs within target sites for miRNAs that are expressed only in the colorectum (the colorectal microRNAome) and having adequate population frequencies. This yielded 12 SNPs that were genotyped in a case-control association study on 717 colorectal cases and 1171 controls from the Czech Republic. RESULTS Statistically significant associations were found between the risk of CRC and the variant alleles of KIAA0182 (rs709805) (odds ratio = 1.57; 95% confidence interval = 1.06-2.78, for the variant homozygotes) and NUP210 genes (rs354476) (odds ratio = 1.36; 95% confidence interval = 1.02-1.82, for the variant homozygotes). CONCLUSIONS The results support the study hypothesis and highlight the importance of SNPs within miRNA-dependent regulatory regions. Further studies on the role exerted by NUP210 and KIAA0182 in colorectal carcinogenesis are warranted.
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Affiliation(s)
- Debora Landi
- Department of Biology, University of Pisa, Pisa, Italy
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239
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Reczko M, Maragkakis M, Alexiou P, Papadopoulos GL, Hatzigeorgiou AG. Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data. Front Genet 2012; 2:103. [PMID: 22303397 PMCID: PMC3265086 DOI: 10.3389/fgene.2011.00103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 12/18/2011] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small regulatory genes regulating gene expression by targeting messenger RNA. Though computational methods for miRNA target prediction are the prevailing means to analyze their function, they still miss a large fraction of the targeted genes and additionally predict a large number of false positives. Here we introduce a novel algorithm called DIANA-microT-ANN which combines multiple novel target site features through an artificial neural network (ANN) and is trained using recently published high-throughput data measuring the change of protein levels after miRNA overexpression, providing positive and negative targeting examples. The features characterizing each miRNA recognition element include binding structure, conservation level, and a specific profile of structural accessibility. The ANN is trained to integrate the features of each recognition element along the 3′untranslated region into a targeting score, reproducing the relative repression fold change of the protein. Tested on two different sets the algorithm outperforms other widely used algorithms and also predicts a significant number of unique and reliable targets not predicted by the other methods. For 542 human miRNAs DIANA-microT-ANN predicts 120000 targets not provided by TargetScan 5.0. The algorithm is freely available at http://microrna.gr/microT-ANN.
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Affiliation(s)
- Martin Reczko
- Institute of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming" Vari, Greece
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240
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Abstract
Research into small non-coding RNAs (ncRNA) has fundamentally transformed our understanding of gene regulatory networks, especially at the post-transcriptional level. Although much is now known about the basic biology of small ncRNAs, our ability to recognize the impact of small ncRNA in disease states is preliminary, and the ability to effectively target them in vivo is very limited. However, given the larger and growing focus on targeting RNAs for disease therapeutics, what we do know about the intrinsic biology of these small RNAs makes them potentially attractive targets for pharmacologic manipulation. With that in mind, this review provides an introduction to the biology of small ncRNA, using microRNA (miRNA) and small nucleolar RNA (snoRNA) as examples.
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241
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Long JM, Lahiri DK. Advances in microRNA experimental approaches to study physiological regulation of gene products implicated in CNS disorders. Exp Neurol 2012; 235:402-18. [PMID: 22245616 DOI: 10.1016/j.expneurol.2011.12.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/13/2011] [Accepted: 12/25/2011] [Indexed: 11/28/2022]
Abstract
The central nervous system (CNS) is a remarkably complex organ system, requiring an equally complex network of molecular pathways controlling the multitude of diverse, cellular activities. Gene expression is a critical node at which regulatory control of molecular networks is implemented. As such, elucidating the various mechanisms employed in the physiological regulation of gene expression in the CNS is important both for establishing a reference for comparison to the diseased state and for expanding the set of validated drug targets available for disease intervention. MicroRNAs (miRNAs) are an abundant class of small RNA that mediates potent inhibitory effects on global gene expression. Recent advances have been made in methods employed to study the contribution of these miRNAs to gene expression. Here we review these latest advances and present a methodological workflow from the perspective of an investigator studying the physiological regulation of a gene of interest. We discuss methods for identifying putative miRNA target sites in a transcript of interest, strategies for validating predicted target sites, assays for detecting miRNA expression, and approaches for disrupting endogenous miRNA function. We consider both advantages and limitations, highlighting certain caveats that inform the suitability of a given method for a specific application. Through careful implementation of the appropriate methodologies discussed herein, we are optimistic that important discoveries related to miRNA participation in CNS physiology and dysfunction are on the horizon.
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Affiliation(s)
- Justin M Long
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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242
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Beveridge NJ, Cairns MJ. MicroRNA dysregulation in schizophrenia. Neurobiol Dis 2011; 46:263-71. [PMID: 22207190 DOI: 10.1016/j.nbd.2011.12.029] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/30/2011] [Accepted: 12/12/2011] [Indexed: 12/15/2022] Open
Abstract
Schizophrenia is a complex neuropsychiatric disorder that involves disturbances in neural circuitry and synaptic function. The exquisite network architecture and capacity for discreet post-synaptic remodeling of neurons requires coordination by an elaborate intracellular network of molecular signal transduction systems. The redundancy of these networks means that many combinations of gene variants have the potential to cause system dysfunction that manifest as related neurobehavioural syndromes. Recent investigation has revealed that posttranscriptional gene regulation and associated small non-coding microRNA (miRNA), are likely to be important factors shaping the topography of these networks. miRNA display complex temporospatial expression patterns in the mammalian brain and have the potential to regulate thousands of target genes by functioning as the specificity factor for intracellular gene-silencing machinery. They are emerging as key regulators of many neurodevelopmental and neurological processes as their dysregulation could lead to pervasive changes in the network structure during development and in the mature brain that are highly significant in the pathophysiology of schizophrenia. This review looks at mounting evidence that mature miRNA levels are altered in both the cerebral cortex and peripheral blood mononuclear cells (PBMCs) in schizophrenia. It also examines compelling evidence that the underlying miRNA biogenesis machinery and miRNA genes themselves are subject to disease-associated genetic mutation and epigenetic influence. Significantly, these changes in miRNA expression and associated machinery may represent new targets for pharmaceutical development, and the identification of miRNA signatures in PBMCs suggest that miRNA biomarkers of schizophrenia may also provide the basis for new clinical diagnostics. These developments have tremendous potential and highlight the significance of this avenue of research.
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Affiliation(s)
- Natalie J Beveridge
- Faculty of Health and the Hunter Medical Research Institute, School of Biomedical Sciences and Pharmacy, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
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243
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vHoT: a database for predicting interspecies interactions between viral microRNA and host genomes. Arch Virol 2011; 157:497-501. [DOI: 10.1007/s00705-011-1181-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 11/19/2011] [Indexed: 01/24/2023]
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244
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Staton AA, Giraldez AJ. Use of target protector morpholinos to analyze the physiological roles of specific miRNA-mRNA pairs in vivo. Nat Protoc 2011; 6:2035-49. [PMID: 22134127 DOI: 10.1038/nprot.2011.423] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) regulate gene expression by pairing with complementary sequences in the 3' untranslated regions (UTRs) of transcripts. Although the molecular mechanism underlying miRNA biogenesis and activity is becoming better understood, determining the physiological role of the interaction of an miRNA with its target remains a challenge. A number of methods have been developed to inhibit individual miRNAs, but it can be difficult to determine which specific targets are responsible for any observed phenotypes. To address this problem, we use target protector (TP) morpholinos that interfere with a single miRNA-mRNA pair by binding specifically to the miRNA target sequence in the 3' UTR. In this protocol, we detail the steps for identifying miRNA targets, validating their regulation and using TPs to interrogate their function in zebrafish. Depending on the biological context, this set of experiments can be completed in 6-8 weeks.
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Affiliation(s)
- Alison A Staton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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245
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Pang RTK, Liu WM, Leung CON, Ye TM, Kwan PCK, Lee KF, Yeung WSB. miR-135A regulates preimplantation embryo development through down-regulation of E3 Ubiquitin Ligase Seven In Absentia Homolog 1A (SIAH1A) expression. PLoS One 2011; 6:e27878. [PMID: 22132158 PMCID: PMC3222661 DOI: 10.1371/journal.pone.0027878] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/27/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNA molecules capable of regulating transcription and translation. Previously, a cluster of miRNAs that are specifically expressed in mouse zygotes but not in oocytes or other preimplantation stages embryos are identified by multiplex real-time polymerase chain reaction-based miRNA profiling. The functional role of one of these zygote-specific miRNAs, miR-135a, in preimplantation embryo development was investigated. METHODOLOGY/PRINCIPAL FINDINGS Microinjection of miR-135a inhibitor suppressed first cell cleavage in more than 30% of the zygotes. Bioinformatics analysis identified E3 Ubiquitin Ligase Seven In Absentia Homolog 1A (Siah1a) as a predicted target of miR-135a. Western blotting and 3'UTR luciferase functional assays demonstrated that miR-135a down-regulated the expression of Siah1 in HeLa cells and in mouse zygotes. Siah1a was expressed in preimplantation embryos and its expression pattern negatively correlated with that of miR-135a. Co-injection of Siah1a-specific antibody with miR-135a inhibitor partially nullified the effect of miR-135a inhibition. Proteasome inhibition by MG-132 revealed that miR-135a regulated proteasomal degradation and potentially controlled the expression of chemokinesin DNA binding protein (Kid). CONCLUSIONS/SIGNIFICANCE The present study demonstrated for the first time that zygotic specific miRNA modulates the first cell cleavage through regulating expression of Siah1a.
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Affiliation(s)
- Ronald T. K. Pang
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
- Centre for Reproduction, Development and Growth, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
| | - Wei-Min Liu
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
- Centre for Reproduction, Development and Growth, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
| | - Carmen O. N. Leung
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
| | - Tian-Min Ye
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
| | - Peter C. K. Kwan
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
| | - Kai-Fai Lee
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
- Centre for Reproduction, Development and Growth, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
| | - William S. B. Yeung
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
- Centre for Reproduction, Development and Growth, The University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
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246
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Carrillo ED, Escobar Y, González G, Hernández A, Galindo JM, García MC, Sánchez JA. Posttranscriptional regulation of the β2-subunit of cardiac L-type Ca2+ channels by MicroRNAs during long-term exposure to isoproterenol in rats. J Cardiovasc Pharmacol 2011; 58:470-8. [PMID: 21753737 DOI: 10.1097/fjc.0b013e31822a789b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION AND METHODS The effects of long-term β-adrenergic administration on the expression levels of the cardiac L-type Ca channel β2 subunit, which regulates channel trafficking and function, were characterized in adult rats. RESULTS Systemic administration of isoproterenol (150 mg·kg·h) for 2 d led to a 50% increase in the ventricular wet weight-to-body weight ratio (mg/g) and of more than two-fold in the expression of actin protein. In contrast, β2 subunit protein levels decreased (down to 49%), while mRNA levels remained unchanged. Furthermore, levels of microRNAs (miRs), including miR-21 and miR-132, were upregulated (7.2 and 7.9 fold, respectively). Transfection of these miRs into HEK293 cells attenuated expression of a luciferase reporter gene controlled by a conserved 3'-untranslated region (UTR) of the β2 subunit (down to 67% and 56%, respectively). Systemic administration of isoproterenol also led to briefer intracellular Ca transients during action potentials measured in isolated cardiomyocytes (down to 65%). CONCLUSION These results suggest that cardiac L-type Ca channel β2 subunit protein expression may be downregulated by miRs in response to long-term activation of β-adrenergic signaling, possibly as an adaptive response in cardiac hypertrophy and sustained β-adrenergic states.
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Affiliation(s)
- Elba D Carrillo
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional, México, DF, México
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Predicting miRNA-mediated gene silencing mode based on miRNA-target duplex features. Comput Biol Med 2011; 42:1-7. [PMID: 22041293 DOI: 10.1016/j.compbiomed.2011.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 09/26/2011] [Accepted: 10/07/2011] [Indexed: 01/08/2023]
Abstract
There are two main mechanisms of miRNA-mediated gene silencing: either mRNA degradation or translational repression. However, the precise mechanism of target mRNAs regulated by miRNA remains unclear. As a complementary approach to experiment, a computational method was proposed to recognize the mechanism of miRNA-mediated gene silencing in human. We have analyzed extensive features correlated with miRNA-mediated silencing mechanism of mRNA. It is found that, the duplex structure, the number of binding sites and the structural accessibility of target site region are effective factors in determining whether a target mRNA is cleaved or only translationally inhibited. An SVM-based classifier was constructed to predict the regulation mode of miRNA based on these informative features. The results indicated that the approach proposed is effective in distinguishing whether a target mRNA is cleaved or translationally inhibited in human. Furthermore, the web server microDoR (http://reprod.njmu.edu.cn/microdor) has been developed and is freely available for users.
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Corrada D, Viti F, Merelli I, Battaglia C, Milanesi L. myMIR: a genome-wide microRNA targets identification and annotation tool. Brief Bioinform 2011; 12:588-600. [PMID: 22021901 DOI: 10.1093/bib/bbr062] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
miRNA target genes prediction represents a crucial step in miRNAs functional characterization. In this context, the challenging issue remains predictions accuracy and recognition of false positive results. In this article myMIR, a web based system for increasing reliability of miRNAs predicted targets lists, is presented. myMIR implements an integrated pipeline for computing ranked miRNA::target lists and provides annotations for narrowing them down. The system relies on knowledge base data, suitably integrated in order to extend the functional characterization of targeted genes to miRNAs, by highlighting the search on over-represented annotation terms. Validation results show a dramatic reduction in the quantity of predictions and an increase in the sensitivity, when compared to other methods. This improves the predictions accuracy and allows the formulation of novel hypotheses on miRNAs functional involvement.
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Affiliation(s)
- Dario Corrada
- Institute for Biomedical Technologies - National Research Council (ITB-CNR), Segrate, Italy.
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249
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Babu SG, Ponia SS, Kumar D, Saxena S. Cellular oncomiR orthologue in EBV oncogenesis. Comput Biol Med 2011; 41:891-8. [PMID: 21880309 DOI: 10.1016/j.compbiomed.2011.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/22/2011] [Accepted: 07/30/2011] [Indexed: 12/19/2022]
Abstract
MicroRNAs are small non-coding RNAs that regulate gene expression at multiple levels. The discovery of virally encoded miRNAs attracted immense attention towards their role in viral replication and pathogenesis. Kaposi's-sarcoma-associated herpes virus encodes miRNA that functions as an orthologue of human cellular miRNA, i.e., hsa-miR-155. Keeping the same view we extended the miRNA-homology search between the miRNAs of humans and Epstein-Barr virus. The In silico analyses shows that EBV encoded miR-BART-5 has a significant 'seed' sequence homology to hsa-miR-18 of humans. Further, the mRNA transcripts of the human genes involved in cellular growth could potentially be targeted by both viral as well as human miRNAs. The known etiological role of hsa-miR-18 as an oncomiR suggests that miR-BART-5 may function as viral oncomiR as observed in EBV-positive gastric carcinoma patients.
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Affiliation(s)
- Sunil G Babu
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India.
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250
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Leone V, D'Angelo D, Ferraro A, Pallante P, Rubio I, Santoro M, Croce CM, Fusco A. A TSH-CREB1-microRNA loop is required for thyroid cell growth. Mol Endocrinol 2011; 25:1819-30. [PMID: 21816899 DOI: 10.1210/me.2011-0014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
MicroRNA (miRNA or miR) are an important class of regulators that participate in such biological functions as development, cell proliferation, differentiation, and apoptosis. The aim of this study was to elucidate the role of miRNA in cell proliferation using a unique cell system, namely thyroid cells that require thyrotropin for their growth. Here, we report the identification of a set of five specific miRNA (miR-1, miR-28-A, miR-290-5p, miR-296-3p, and miR-297a), whose down-regulation by thyrotropin is required for thyroid cell growth. In fact, overexpression of these miRNA negatively affects cell growth. We show that three of these miRNA target cAMP-responsive element binding protein (CREB)1, a thyrotropin-activated transcription factor, and that CREB1 binds the regulatory regions of the down-regulated miRNA. Hence, these data indicate that a synergistic loop involving thyrotropin, CREB1, and miRNA is required for thyroid cell proliferation.
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Affiliation(s)
- Vincenza Leone
- Istituto di Endocrinologia ed Oncologia Sperimentale del Consiglio Nazionale delle Ricerche, Dipartimento di Biologia e Patologia Cellulare e Molecolare, Facoltà di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli Federico II, Naples, Italy
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