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A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions

BACKGROUND: MicroRNAs are ~17–24 nt. noncoding RNAs found in all eukaryotes that degrade messenger RNAs via RNA interference (if they bind in a perfect or near-perfect complementarity to the target mRNA), or arrest translation (if the binding is imperfect). Several microRNA targets have been identif...

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Detalles Bibliográficos
Autores principales: Smalheiser, Neil R, Torvik, Vetle I
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2004
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC523849/
https://www.ncbi.nlm.nih.gov/pubmed/15453917
http://dx.doi.org/10.1186/1471-2105-5-139
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author Smalheiser, Neil R
Torvik, Vetle I
author_facet Smalheiser, Neil R
Torvik, Vetle I
author_sort Smalheiser, Neil R
collection PubMed
description BACKGROUND: MicroRNAs are ~17–24 nt. noncoding RNAs found in all eukaryotes that degrade messenger RNAs via RNA interference (if they bind in a perfect or near-perfect complementarity to the target mRNA), or arrest translation (if the binding is imperfect). Several microRNA targets have been identified in lower organisms, but only one mammalian microRNA target has yet been validated experimentally. RESULTS: We carried out a population-wide statistical analysis of how human microRNAs interact complementarily with human mRNAs, looking for characteristics that differ significantly as compared with scrambled control sequences. These characteristics were used to identify a set of 71 outlier mRNAs unlikely to have been hit by chance. Unlike the case in C. elegans and Drosophila, many human microRNAs exhibited long exact matches (10 or more bases in a row), up to and including perfect target complementarity. Human microRNAs hit outlier mRNAs within the protein coding region about 2/3 of the time. And, the stretches of perfect complementarity within microRNA hits onto outlier mRNAs were not biased near the 5'-end of the microRNA. In several cases, an individual microRNA hit multiple mRNAs that belonged to the same functional class. CONCLUSIONS: The analysis supports the notion that sequence complementarity is the basis by which microRNAs recognize their biological targets, but raises the possibility that human microRNA-mRNA target interactions follow different rules than have been previously characterized in Drosophila and C. elegans.
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spelling pubmed-5238492004-10-22 A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions Smalheiser, Neil R Torvik, Vetle I BMC Bioinformatics Research Article BACKGROUND: MicroRNAs are ~17–24 nt. noncoding RNAs found in all eukaryotes that degrade messenger RNAs via RNA interference (if they bind in a perfect or near-perfect complementarity to the target mRNA), or arrest translation (if the binding is imperfect). Several microRNA targets have been identified in lower organisms, but only one mammalian microRNA target has yet been validated experimentally. RESULTS: We carried out a population-wide statistical analysis of how human microRNAs interact complementarily with human mRNAs, looking for characteristics that differ significantly as compared with scrambled control sequences. These characteristics were used to identify a set of 71 outlier mRNAs unlikely to have been hit by chance. Unlike the case in C. elegans and Drosophila, many human microRNAs exhibited long exact matches (10 or more bases in a row), up to and including perfect target complementarity. Human microRNAs hit outlier mRNAs within the protein coding region about 2/3 of the time. And, the stretches of perfect complementarity within microRNA hits onto outlier mRNAs were not biased near the 5'-end of the microRNA. In several cases, an individual microRNA hit multiple mRNAs that belonged to the same functional class. CONCLUSIONS: The analysis supports the notion that sequence complementarity is the basis by which microRNAs recognize their biological targets, but raises the possibility that human microRNA-mRNA target interactions follow different rules than have been previously characterized in Drosophila and C. elegans. BioMed Central 2004-09-28 /pmc/articles/PMC523849/ /pubmed/15453917 http://dx.doi.org/10.1186/1471-2105-5-139 Text en Copyright © 2004 Smalheiser and Torvik; licensee BioMed Central Ltd.
spellingShingle Research Article
Smalheiser, Neil R
Torvik, Vetle I
A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions
title A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions
title_full A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions
title_fullStr A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions
title_full_unstemmed A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions
title_short A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions
title_sort population-based statistical approach identifies parameters characteristic of human microrna-mrna interactions
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC523849/
https://www.ncbi.nlm.nih.gov/pubmed/15453917
http://dx.doi.org/10.1186/1471-2105-5-139
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