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Fu Y, Lee I, Lee YS, Bao X. Small Non-coding Transfer RNA-Derived RNA Fragments (tRFs): Their Biogenesis, Function and Implication in Human Diseases. Genomics Inform 2015; 13:94-101. [PMID: 26865839 PMCID: PMC4742329 DOI: 10.5808/gi.2015.13.4.94] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 12/19/2015] [Accepted: 12/21/2015] [Indexed: 02/06/2023] Open
Abstract
tRNA-derived RNA fragments (tRFs) are an emerging class of non-coding RNAs (ncRNAs). A growing number of reports have shown that tRFs are not random degradation products but are functional ncRNAs made of specific tRNA cleavage. They play regulatory roles in several biological contexts such as cancer, innate immunity, stress responses, and neurological disorders. In this review, we summarize the biogenesis and functions of tRFs.
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Affiliation(s)
- Yu Fu
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Yong Sun Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xiaoyong Bao
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA.; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.; The Institute of Translational Science, University of Texas Medical Branch, Galveston, TX 77555, USA.; The Institute for Human Infections & Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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MicroRNAs and their applications in kidney diseases. Pediatr Nephrol 2015; 30:727-40. [PMID: 24928414 PMCID: PMC4265577 DOI: 10.1007/s00467-014-2867-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/12/2014] [Accepted: 05/21/2014] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs that employ classic Watson-Crick base-pairing to identify their target genes, ultimately resulting in destabilization of their target mRNAs and/or inhibition of their translation. The role of miRNAs in a wide range of human diseases, including those afflicting the kidney, has been intensely investigated. However, there is still a vast dearth of knowledge regarding their specific mode of action and therapeutic effects in various kidney diseases. This review discusses the latest efforts to further our understanding of the basic biology of miRNAs, their impact on various kidney diseases and their potential as novel biomarkers and therapeutic agents. We initially provide an overview of miRNA biology and the canonical pathway implicated in their biogenesis. We then discuss commonly employed experimental strategies for miRNA research and highlight some of the newly described state-of-the-art technologies to identify miRNAs and their target genes. Finally, we carefully examine the emerging role of miRNAs in the pathogenesis of various kidney diseases.
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Wilflingseder J, Reindl-Schwaighofer R, Sunzenauer J, Kainz A, Heinzel A, Mayer B, Oberbauer R. MicroRNAs in kidney transplantation. Nephrol Dial Transplant 2014; 30:910-7. [PMID: 25170095 DOI: 10.1093/ndt/gfu280] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/27/2014] [Indexed: 12/13/2022] Open
Abstract
The discovery of novel classes of non-coding RNAs (ncRNAs) has revolutionized medicine. Long thought to be a mere cellular housekeeper, surprising functions have recently been uncovered. MicroRNAs (miRNAs), are a representative of the class of short ncRNAs, play a fundamental role in the control of DNA and protein biosynthesis and activity as well as pathology. Currently, miRNAs are being investigated as diagnostic and prognostic markers and potential therapeutic targets in kidney transplantation for such indolent processes as ischaemia-reperfusion injury, humoral rejection or viral infections. It is realistic to believe that monitoring of renal allograft recipients in the future will include genome-wide miRNA profiling of biological fluids. Based on these individual profiles, an informed decision on therapeutic consequences will be possible. A first success with a specific suppression of miRNAs by antisense oligonucleotides was achieved in experimental studies of reperfusion injury and humoral rejection. Proof of this concept in men comes from studies in such indolent viral infections as Ebola and hepatitis C, where anti-miR therapy led to sustained viral clearance. In this review, we summarize the basis of the recent ncRNA revolution and its implication for kidney transplantation.
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Affiliation(s)
- Julia Wilflingseder
- Department of Nephrology and Dialysis, Medical University Vienna, Vienna, Austria Department of Nephrology, KH Elisabethinen, Linz, Austria
| | | | | | - Alexander Kainz
- Department of Nephrology and Dialysis, Medical University Vienna, Vienna, Austria Department of Nephrology, KH Elisabethinen, Linz, Austria
| | | | - Bernd Mayer
- emergentec biodevelopment GmbH, Vienna, Austria
| | - Rainer Oberbauer
- Department of Nephrology and Dialysis, Medical University Vienna, Vienna, Austria Department of Nephrology, KH Elisabethinen, Linz, Austria
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Emerging nanodelivery strategies of RNAi molecules for colon cancer therapy: preclinical developments. Ther Deliv 2012; 3:1117-30. [DOI: 10.4155/tde.12.89] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Although local colonic delivery is achievable through several strategies, colon cancer is still considered one of the leading causes of death worldwide. Failure of chemotherapeutics to exhibit efficient anticancer activity might be attributed to the development of multidrug resistance (MDR) mechanisms including the overexpression of certain oncogenes such as MDR1/P-gp. One of the major reasons for the shortcoming of P-gp inhibitors in clinic is the nonspecific distribution of them to nontarget organs, which leads to reduced elimination and increased toxicity of its substrates including anticancer agents. Numerous studies have demonstrated the effectiveness of gene-silencing approaches in reversing the P-gp-mediated MDR. However, none have reached clinical trials yet. Several drug-delivery systems have been investigated primarily to address P-gp and the observed improved anticancer efficacy suggests that nanomedicine provides new opportunities to overcome MDR in cancer. In this review, novel therapeutic strategies for colon cancer therapy will be discussed in the context of P-gp inhibition by low-molecular-weight agents and RNAi molecules.
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Hamilton SK, Sims AL, Donavan J, Harth E. Non-viral siRNA delivery vectors: dendritic molecular transporter and molecular transporter nanovectors for target gene silencing. Polym Chem 2011. [DOI: 10.1039/c0py00342e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Alshamsan A, Hamdy S, Samuel J, El-Kadi AO, Lavasanifar A, Uludağ H. The induction of tumor apoptosis in B16 melanoma following STAT3 siRNA delivery with a lipid-substituted polyethylenimine. Biomaterials 2010; 31:1420-8. [DOI: 10.1016/j.biomaterials.2009.11.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 11/02/2009] [Indexed: 12/21/2022]
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Kuzawa CW, Sweet E. Epigenetics and the embodiment of race: Developmental origins of US racial disparities in cardiovascular health. Am J Hum Biol 2009; 21:2-15. [DOI: 10.1002/ajhb.20822] [Citation(s) in RCA: 428] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Abstract
Within the past few years, studies on microRNA (miRNA) and cancer have burst onto the scene. Profiling of the miRNome (global miRNA expression levels) has become prevalent, and abundant miRNome data are currently available for various cancers. The pattern of miRNA expression can be correlated with cancer type, stage, and other clinical variables, so miRNA profiling can be used as a tool for cancer diagnosis and prognosis. miRNA expression analyses also suggest oncogenic (or tumor-suppressive) roles of miRNAs. miRNAs play roles in almost all aspects of cancer biology, such as proliferation, apoptosis, invasion/metastasis, and angiogenesis. Given that many miRNAs are deregulated in cancers but have not yet been further studied, it is expected that more miRNAs will emerge as players in the etiology and progression of cancer. Here we also discuss miRNAs as a tool for cancer therapy.
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Affiliation(s)
- Yong Sun Lee
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
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Alshamsan A, Haddadi A, Incani V, Samuel J, Lavasanifar A, Uludağ H. Formulation and Delivery of siRNA by Oleic Acid and Stearic Acid Modified Polyethylenimine. Mol Pharm 2008; 6:121-33. [DOI: 10.1021/mp8000815] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Aws Alshamsan
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton T6G 2N8, Canada, Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2V2, Canada, and Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton T6G 2G6, Canada
| | - Azita Haddadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton T6G 2N8, Canada, Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2V2, Canada, and Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton T6G 2G6, Canada
| | - Vanessa Incani
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton T6G 2N8, Canada, Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2V2, Canada, and Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton T6G 2G6, Canada
| | - John Samuel
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton T6G 2N8, Canada, Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2V2, Canada, and Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton T6G 2G6, Canada
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton T6G 2N8, Canada, Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2V2, Canada, and Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton T6G 2G6, Canada
| | - Hasan Uludağ
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton T6G 2N8, Canada, Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2V2, Canada, and Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton T6G 2G6, Canada
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Abstract
To counteract the immune system in parasitic hosts, some viruses encode proteins to suppress the RNA interference (RNAi) effect. In this report, we established two RNAi systems to be easily observed with strong and obvious effect. The function of the P19 of tomato bushy stunt virus, which suppresses RNAi in mammal cells, was then studied using these two systems. Short hairpin RNAs targeting green fluorescence protein (pshRNA-GFP) and firefly luciferase (pshRNA-luc) were designed and inserted into a eukaryotic transcriptional vector pTZU6+1, respectively. The shRNA expressing vectors were co-transfected with plasmids containing the target gene with or without P19. The GFP expression level was assayed by fluorescence microscopy, Western blotting and RT-PCR. The luciferase expression level was analyzed by the dual-luciferase assay system. pshRNA designed in this study down-regulated the target gene specifically and efficiently, with a decrease of expression of both genes of about 70%, respectively. When P19 was introduced into the RNAi systems, the expression of both GFP and the luciferase were mostly recovered compared with the control groups. The RNAi systems of GFP and luciferase were constructed successfully, demonstrating that P19 of tomato bushy stunt virus has the ability to counteract the RNAi effect induced by shRNA in mammal cells.
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Affiliation(s)
- Paul D Berk
- The Division of Digestive Liver Diseases, Department of Medicine, Columbia University Medical Center, New York, NY
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Abstract
MOTIVATION Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. RESULTS In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. AVAILABILITY The source code is available under GNU Public License at the supplementary web site.
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Affiliation(s)
- Zasha Weinberg
- Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA.
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Affiliation(s)
- Yoriko Saito
- Blood Transfusion Service, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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Perkins DO, Jeffries C, Sullivan P. Expanding the 'central dogma': the regulatory role of nonprotein coding genes and implications for the genetic liability to schizophrenia. Mol Psychiatry 2005; 10:69-78. [PMID: 15381925 DOI: 10.1038/sj.mp.4001577] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
It is now evident that nonprotein coding RNA (ncRNA) plays a critical role in regulating the timing and rate of protein translation. The potential importance of ncRNAs is suggested by the observation that the complexity of an organism is poorly correlated with its number of protein coding genes, yet highly correlated with its number of ncRNA genes, and that in the human genome only a small fraction (2-3%) of genetic transcripts are actually translated into proteins. In this review, we discuss several examples of known RNA mechanisms for the regulation of protein synthesis. We then discuss the possibility that ncRNA regulation of schizophrenia risk genes may underlie the diverse findings of genetic linkage studies including that protein-altering gene polymorphisms are not generally found in schizophrenia. Thus, inadequate or mistimed expression of a functional protein may occur either due to mutation or other dysfunction of the DNA coding base pair sequence, leading to a dysfunctional protein, or due to post-transcriptional events such as abnormal ncRNA regulation of a normal gene. One or more 'schizophrenia disease genes' may turn out to include abnormal transcriptional units that code for RNA regulators of protein coding gene expression or to be proximal to such units, rather than to be abnormalities in the protein coding gene itself. Understanding the genetics of schizophrenia and other complex neuropsychiatric disorders might very well include consideration of RNA and epigenetic regulation of protein expression in addition to polymorphisms of the protein coding gene.
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Affiliation(s)
- D O Perkins
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Abstract
This article summarizes the general principles of selections and screens in Escherichia coli. The focus is on the lac operon, owing to its inherent simplicity and versatility. Examples of different strategies for mutagenesis and mutant discovery are described. In particular, the usefulness and effectiveness of simple colour-based screens are illustrated. The power of lac genetics can be applied to almost any bacterial system with gene fusions that hook any gene of interest to lacZ, which is the structural gene that encodes beta-galactosidase. The diversity of biological processes that can be studied with lac genetics is remarkable and includes DNA metabolism, gene regulation and signal transduction, protein localization and folding, and even electron transport.
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Affiliation(s)
- Howard A Shuman
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York 10032, USA
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