Abstract
MicroRNAs (miRNAs) comprise a recently discovered class of small, non-coding RNA molecules of 21-25 nucleotides in length that regulate the gene expression by base-pairing with the transcripts of their targets i.e. proteincoding genes, leading to down-regulation or repression of the target genes. However, target gene activation has also been described. miRNAs are involved in diverse regulatory pathways, including control of developmental timing, apoptosis, cell proliferation, cell differentiation, modulation of immune response to macrophages, and organ development and are associated with many diseases, such as cancer. Computational prediction of miRNA targets is much more challenging in animals than in plants, because animal miRNAs often perform imperfect base-pairing with their target sites, unlike plant miRNAs which almost always bind their targets with near perfect complementarity. In the past years, a large number of target prediction programs and databases on experimentally validated information have been developed for animal miRNAs to fulfil the need of experimental scientists conducting miRNA research. In this review we first succinctly describe the prediction criteria (rules or principles) adapted by prediction algorithms to generate possible miRNA binding site interactions and introduce most relevant algorithms, and databases. We then summarize their applications with the help of some previously published studies. We further provide experimentally validated functional binding sites outside 3’-UTR region of target mRNAs and the resources which offer such predictions. Finally, the issue of experimental validation of miRNA binding sites will be briefly discussed.
Keywords: microRNAs, miRWalk, Target prediction, Promoter, CDS, UTR, Prediction algorithm, Database
Current Genomics
Title:In-Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions
Volume: 14 Issue: 2
Author(s): Harsh Dweep, Carsten Sticht and Norbert Gretz
Affiliation:
Keywords: microRNAs, miRWalk, Target prediction, Promoter, CDS, UTR, Prediction algorithm, Database
Abstract: MicroRNAs (miRNAs) comprise a recently discovered class of small, non-coding RNA molecules of 21-25 nucleotides in length that regulate the gene expression by base-pairing with the transcripts of their targets i.e. proteincoding genes, leading to down-regulation or repression of the target genes. However, target gene activation has also been described. miRNAs are involved in diverse regulatory pathways, including control of developmental timing, apoptosis, cell proliferation, cell differentiation, modulation of immune response to macrophages, and organ development and are associated with many diseases, such as cancer. Computational prediction of miRNA targets is much more challenging in animals than in plants, because animal miRNAs often perform imperfect base-pairing with their target sites, unlike plant miRNAs which almost always bind their targets with near perfect complementarity. In the past years, a large number of target prediction programs and databases on experimentally validated information have been developed for animal miRNAs to fulfil the need of experimental scientists conducting miRNA research. In this review we first succinctly describe the prediction criteria (rules or principles) adapted by prediction algorithms to generate possible miRNA binding site interactions and introduce most relevant algorithms, and databases. We then summarize their applications with the help of some previously published studies. We further provide experimentally validated functional binding sites outside 3’-UTR region of target mRNAs and the resources which offer such predictions. Finally, the issue of experimental validation of miRNA binding sites will be briefly discussed.
Export Options
About this article
Cite this article as:
Dweep Harsh, Sticht Carsten and Gretz Norbert, In-Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions, Current Genomics 2013; 14 (2) . https://dx.doi.org/10.2174/1389202911314020005
DOI https://dx.doi.org/10.2174/1389202911314020005 |
Print ISSN 1389-2029 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5488 |
Call for Papers in Thematic Issues
Current Genomics in Cardiovascular Research
Cardiovascular diseases are the main cause of death in the world, in recent years we have had important advances in the interaction between cardiovascular disease and genomics. In this Research Topic, we intend for researchers to present their results with a focus on basic, translational and clinical investigations associated with ...read more
Deep learning in Single Cell Analysis
The field of biology is undergoing a revolution in our ability to study individual cells at the molecular level, and to integrate data from multiple sources and modalities. This has been made possible by advances in technologies for single-cell sequencing, multi-omics profiling, spatial transcriptomics, and high-throughput imaging, as well as ...read more
New insights on Pediatric Tumors and Associated Cancer Predisposition Syndromes
Because of the broad spectrum of children cancer susceptibility, the diagnosis of cancer risk syndromes in children is rarely used in direct cancer treatment. The field of pediatric cancer genetics and genomics will only continue to expand as a result of increasing use of genetic testing tools. It's possible that ...read more
Related Journals
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements
Related Articles
-
Integrated Analysis of mRNA-seq and miRNA-seq to Identify c-MYC, YAP1 and miR-3960 as Major Players in the Anticancer Effects of Caffeic Acid Phenethyl Ester in Human Small Cell Lung Cancer Cell Line
Current Gene Therapy Synthesis of New Thiazolyl-Pyrazoline Derivatives and Evaluation of Their Antimicrobial, Cytotoxic and Genotoxic Effects
Letters in Drug Design & Discovery PLK1 Inhibition: Prospective Role for the Treatment of Pediatric Tumors
Current Drug Targets ABC Transporters in Extrahepatic Tissues: Pharmacological Regulation in Heart and Intestine
Current Medicinal Chemistry Zinc, Metallothioneins and Longevity: Interrelationships with Niacin and Selenium
Current Pharmaceutical Design Molecular Mechanisms and Proposed Targets for Selected Anticancer Gold Compounds
Current Topics in Medicinal Chemistry Toll Like Receptors Signaling Pathways as a Target for Therapeutic Interventions
Current Signal Transduction Therapy Do we Need Maintenance Chemotherapy in Advanced NSCLC in the Era of Immune and Targeted Therapy?
Current Cancer Therapy Reviews Irinotecan for Treatment of Childhood Cancers: A Promising Therapeutic Partner
Current Cancer Therapy Reviews SUV39H1-Mediated <i>DNMT1</i> is Involved in the Epigenetic Regulation of Smad3 in Cervical Cancer
Anti-Cancer Agents in Medicinal Chemistry Cranberry as Promising Natural Source of Potential Anticancer Agents: Current Evidence and Future Perspectives
Anti-Cancer Agents in Medicinal Chemistry On the Involvement of H2S in Nitroso Signaling and Other Mechanisms of H2S Action
Current Pharmaceutical Biotechnology The Potential Anti-Tumorigenic and Anti-Metastatic Side of the Proprotein Convertases Inhibitors
Recent Patents on Anti-Cancer Drug Discovery Global Gene Expression in Classification, Pathogenetic Understanding and Identification of Therapeutic Targets in Acute Myeloid Leukemia
Current Pharmaceutical Biotechnology The Pharmacological Treatment of Cachexia
Current Drug Targets Dasatinib in the Treatment of Chronic Myeloid Leukemia
Current Signal Transduction Therapy Advances in DNA-Ligands with Groove Binding, Intercalating and/or Alkylating Activity: Chemistry, DNA-Binding and Biology
Current Medicinal Chemistry Microwave-assisted Cycloaddition Reactions in Carbo- and Heterocyclic Chemistry
Current Organic Chemistry PET Studies on P-Glycoprotein Function in the Blood-Brain Barrier: How it Affects Uptake and Binding of Drugs within the CNS
Current Pharmaceutical Design The Role of Tumor Suppressor DLC-1: Far From Clear
Anti-Cancer Agents in Medicinal Chemistry