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Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features

MicroRNAs (small ~22 nucleotide long non-coding endogenous RNAs) have recently attracted immense attention as critical regulators of gene expression in multi-cellular eukaryotes, especially in humans. Recent studies have proved that viruses also express microRNAs, which are thought to contribute to...

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Detalles Bibliográficos
Autores principales: Kumar, Shiva, Ansari, Faraz A, Scaria, Vinod
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743665/
https://www.ncbi.nlm.nih.gov/pubmed/19691855
http://dx.doi.org/10.1186/1743-422X-6-129
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author Kumar, Shiva
Ansari, Faraz A
Scaria, Vinod
author_facet Kumar, Shiva
Ansari, Faraz A
Scaria, Vinod
author_sort Kumar, Shiva
collection PubMed
description MicroRNAs (small ~22 nucleotide long non-coding endogenous RNAs) have recently attracted immense attention as critical regulators of gene expression in multi-cellular eukaryotes, especially in humans. Recent studies have proved that viruses also express microRNAs, which are thought to contribute to the intricate mechanisms of host-pathogen interactions. Computational predictions have greatly accelerated the discovery of microRNAs. However, most of these widely used tools are dependent on structural features and sequence conservation which limits their use in discovering novel virus expressed microRNAs and non-conserved eukaryotic microRNAs. In this work an efficient prediction method is developed based on the hypothesis that sequence and structure features which discriminate between host microRNA precursor hairpins and pseudo microRNAs are shared by viral microRNA as they depend on host machinery for the processing of microRNA precursors. The proposed method has been found to be more efficient than recently reported ab-initio methods for predicting viral microRNAs and microRNAs expressed by mammals.
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spelling pubmed-27436652009-09-15 Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features Kumar, Shiva Ansari, Faraz A Scaria, Vinod Virol J Short Report MicroRNAs (small ~22 nucleotide long non-coding endogenous RNAs) have recently attracted immense attention as critical regulators of gene expression in multi-cellular eukaryotes, especially in humans. Recent studies have proved that viruses also express microRNAs, which are thought to contribute to the intricate mechanisms of host-pathogen interactions. Computational predictions have greatly accelerated the discovery of microRNAs. However, most of these widely used tools are dependent on structural features and sequence conservation which limits their use in discovering novel virus expressed microRNAs and non-conserved eukaryotic microRNAs. In this work an efficient prediction method is developed based on the hypothesis that sequence and structure features which discriminate between host microRNA precursor hairpins and pseudo microRNAs are shared by viral microRNA as they depend on host machinery for the processing of microRNA precursors. The proposed method has been found to be more efficient than recently reported ab-initio methods for predicting viral microRNAs and microRNAs expressed by mammals. BioMed Central 2009-08-20 /pmc/articles/PMC2743665/ /pubmed/19691855 http://dx.doi.org/10.1186/1743-422X-6-129 Text en Copyright © 2009 Kumar et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Short Report
Kumar, Shiva
Ansari, Faraz A
Scaria, Vinod
Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features
title Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features
title_full Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features
title_fullStr Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features
title_full_unstemmed Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features
title_short Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features
title_sort prediction of viral microrna precursors based on human microrna precursor sequence and structural features
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743665/
https://www.ncbi.nlm.nih.gov/pubmed/19691855
http://dx.doi.org/10.1186/1743-422X-6-129
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