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RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles
Tandem stretches of guanines can associate in hydrogen-bonded arrays to form G-quadruplexes, which are stabilized by K(+) ions. Using computational methods, we searched for G-Quadruplex Sequence (GQS) patterns in the model plant species Arabidopsis thaliana. We found ∼1200 GQS with a G(3) repeat seq...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001093/ https://www.ncbi.nlm.nih.gov/pubmed/20860998 http://dx.doi.org/10.1093/nar/gkq804 |
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author | Mullen, Melissa A. Olson, Kalee J. Dallaire, Paul Major, François Assmann, Sarah M. Bevilacqua, Philip C. |
author_facet | Mullen, Melissa A. Olson, Kalee J. Dallaire, Paul Major, François Assmann, Sarah M. Bevilacqua, Philip C. |
author_sort | Mullen, Melissa A. |
collection | PubMed |
description | Tandem stretches of guanines can associate in hydrogen-bonded arrays to form G-quadruplexes, which are stabilized by K(+) ions. Using computational methods, we searched for G-Quadruplex Sequence (GQS) patterns in the model plant species Arabidopsis thaliana. We found ∼1200 GQS with a G(3) repeat sequence motif, most of which are located in the intergenic region. Using a Markov modeled genome, we determined that GQS are significantly underrepresented in the genome. Additionally, we found ∼43 000 GQS with a G(2) repeat sequence motif; notably, 80% of these were located in genic regions, suggesting that these sequences may fold at the RNA level. Gene Ontology functional analysis revealed that GQS are overrepresented in genes encoding proteins of certain functional categories, including enzyme activity. Conversely, GQS are underrepresented in other categories of genes, notably those for non-coding RNAs such as tRNAs and rRNAs. We also find that genes that are differentially regulated by drought are significantly more likely to contain a GQS. CD-detected K(+) titrations performed on representative RNAs verified formation of quadruplexes at physiological K(+) concentrations. Overall, this study indicates that GQS are present at unique locations in Arabidopsis and that folding of RNA GQS may play important roles in regulating gene expression. |
format | Text |
id | pubmed-3001093 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30010932010-12-13 RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles Mullen, Melissa A. Olson, Kalee J. Dallaire, Paul Major, François Assmann, Sarah M. Bevilacqua, Philip C. Nucleic Acids Res Genomics Tandem stretches of guanines can associate in hydrogen-bonded arrays to form G-quadruplexes, which are stabilized by K(+) ions. Using computational methods, we searched for G-Quadruplex Sequence (GQS) patterns in the model plant species Arabidopsis thaliana. We found ∼1200 GQS with a G(3) repeat sequence motif, most of which are located in the intergenic region. Using a Markov modeled genome, we determined that GQS are significantly underrepresented in the genome. Additionally, we found ∼43 000 GQS with a G(2) repeat sequence motif; notably, 80% of these were located in genic regions, suggesting that these sequences may fold at the RNA level. Gene Ontology functional analysis revealed that GQS are overrepresented in genes encoding proteins of certain functional categories, including enzyme activity. Conversely, GQS are underrepresented in other categories of genes, notably those for non-coding RNAs such as tRNAs and rRNAs. We also find that genes that are differentially regulated by drought are significantly more likely to contain a GQS. CD-detected K(+) titrations performed on representative RNAs verified formation of quadruplexes at physiological K(+) concentrations. Overall, this study indicates that GQS are present at unique locations in Arabidopsis and that folding of RNA GQS may play important roles in regulating gene expression. Oxford University Press 2010-12 2010-09-21 /pmc/articles/PMC3001093/ /pubmed/20860998 http://dx.doi.org/10.1093/nar/gkq804 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genomics Mullen, Melissa A. Olson, Kalee J. Dallaire, Paul Major, François Assmann, Sarah M. Bevilacqua, Philip C. RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles |
title | RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles |
title_full | RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles |
title_fullStr | RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles |
title_full_unstemmed | RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles |
title_short | RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles |
title_sort | rna g-quadruplexes in the model plant species arabidopsis thaliana: prevalence and possible functional roles |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001093/ https://www.ncbi.nlm.nih.gov/pubmed/20860998 http://dx.doi.org/10.1093/nar/gkq804 |
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