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
-
Ceramide Kinase and the Ceramide-1-Phosphate/cPLA2α Interaction as a Therapeutic Target
Current Drug Targets SYNTHESIS AND APPLICATIONS OF Fe3O4/SiO2 CORE-SHELL MATERIALS
Current Pharmaceutical Design Role of Stem Cells in Normal Liver and Cancer
Anti-Cancer Agents in Medicinal Chemistry General and Recent Aspects of the Chemistry and Structure Activity Relationships of Taxoids
Current Pharmaceutical Design Caffeic Acid, A Versatile Pharmacophore: An Overview
Mini-Reviews in Medicinal Chemistry Chitosan - A Potential Polymer to Prepare Anticancer Drug Delivery Systems: Patent Review
Recent Patents on Anti-Cancer Drug Discovery Mapping the High Throughput SEREX Technology Screening for Novel Tumor Antigens
Combinatorial Chemistry & High Throughput Screening Discovery of 4-Aryl-4H-Chromenes as Potent Apoptosis Inducers Using a Cell- and Caspase-Based Anti-Cancer Screening Apoptosis Program (ASAP): SAR Studies and the Identification of Novel Vascular Disrupting Agents
Anti-Cancer Agents in Medicinal Chemistry Transcriptional Regulation of Antimicrobial Host Defense Peptides
Current Protein & Peptide Science The Potency of Refined Mouse Models: Implications for Clinical Trials
Current Cancer Therapy Reviews Nanoparticles for Cancer Targeting: Current and Future Directions
Current Drug Delivery The NK-1 Receptor is Involved in the Antitumoural Action of L-733,060 and in the Mitogenic Action of Substance P on Human Pancreatic Cancer Cell Lines
Letters in Drug Design & Discovery Chronic Migraineurs Form Carboxyhemefibrinogen and Iron-Bound Fibrinogen
CNS & Neurological Disorders - Drug Targets Bisacylimidoselenocarbamates Cause G2/M Arrest Associated with the Modulation of CDK1 and Chk2 in Human Breast Cancer MCF-7 Cells
Current Medicinal Chemistry Targeting Proteasomes with Naturally Occurring Compounds in Cancer Treatment
Current Cancer Drug Targets Genetic Variants in Genes Involved in Mechanisms of Chemoresistance to Anticancer Drugs
Current Cancer Drug Targets A Review on Exploring Better Safety Prospects in Managing Cancer using Liposomal Combinations of Food Bioactive Compounds and Anticancer Drugs: Combisomes
Current Drug Delivery Pharmacological Modulation of Caspase Activation
Current Medicinal Chemistry - Anti-Inflammatory & Anti-Allergy Agents Baicalin-induced Cytotoxicity and Apoptosis in Multidrug-resistant MC3/5FU Mucoepidermoid Carcinoma Cell Line
Letters in Drug Design & Discovery Patent Selections
Recent Patents on Chemical Engineering