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Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
BACKGROUND: MiRNAs have emerged as key regulators of stress response in plants, suggesting their potential as candidates for knock-in/out to improve stress tolerance in agricultural crops. Although diverse assays have been performed, systematic and detailed studies of miRNA expression and function d...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379984/ https://www.ncbi.nlm.nih.gov/pubmed/30777009 http://dx.doi.org/10.1186/s12870-019-1679-0 |
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author | Sanz-Carbonell, Alejandro Marques, María Carmen Bustamante, Antonio Fares, Mario A. Rodrigo, Guillermo Gomez, Gustavo |
author_facet | Sanz-Carbonell, Alejandro Marques, María Carmen Bustamante, Antonio Fares, Mario A. Rodrigo, Guillermo Gomez, Gustavo |
author_sort | Sanz-Carbonell, Alejandro |
collection | PubMed |
description | BACKGROUND: MiRNAs have emerged as key regulators of stress response in plants, suggesting their potential as candidates for knock-in/out to improve stress tolerance in agricultural crops. Although diverse assays have been performed, systematic and detailed studies of miRNA expression and function during exposure to multiple environments in crops are limited. RESULTS: Here, we present such pioneering analysis in melon plants in response to seven biotic and abiotic stress conditions. Deep-sequencing and computational approaches have identified twenty-four known miRNAs whose expression was significantly altered under at least one stress condition, observing that down-regulation was preponderant. Additionally, miRNA function was characterized by high scale degradome assays and quantitative RNA measurements over the intended target mRNAs, providing mechanistic insight. Clustering analysis provided evidence that eight miRNAs showed a broad response range under the stress conditions analyzed, whereas another eight miRNAs displayed a narrow response range. Transcription factors were predominantly targeted by stress-responsive miRNAs in melon. Furthermore, our results show that the miRNAs that are down-regulated upon stress predominantly have as targets genes that are known to participate in the stress response by the plant, whereas the miRNAs that are up-regulated control genes linked to development. CONCLUSION: Altogether, this high-resolution analysis of miRNA-target interactions, combining experimental and computational work, Illustrates the close interplay between miRNAs and the response to diverse environmental conditions, in melon. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1679-0) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6379984 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-63799842019-02-28 Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon Sanz-Carbonell, Alejandro Marques, María Carmen Bustamante, Antonio Fares, Mario A. Rodrigo, Guillermo Gomez, Gustavo BMC Plant Biol Research Article BACKGROUND: MiRNAs have emerged as key regulators of stress response in plants, suggesting their potential as candidates for knock-in/out to improve stress tolerance in agricultural crops. Although diverse assays have been performed, systematic and detailed studies of miRNA expression and function during exposure to multiple environments in crops are limited. RESULTS: Here, we present such pioneering analysis in melon plants in response to seven biotic and abiotic stress conditions. Deep-sequencing and computational approaches have identified twenty-four known miRNAs whose expression was significantly altered under at least one stress condition, observing that down-regulation was preponderant. Additionally, miRNA function was characterized by high scale degradome assays and quantitative RNA measurements over the intended target mRNAs, providing mechanistic insight. Clustering analysis provided evidence that eight miRNAs showed a broad response range under the stress conditions analyzed, whereas another eight miRNAs displayed a narrow response range. Transcription factors were predominantly targeted by stress-responsive miRNAs in melon. Furthermore, our results show that the miRNAs that are down-regulated upon stress predominantly have as targets genes that are known to participate in the stress response by the plant, whereas the miRNAs that are up-regulated control genes linked to development. CONCLUSION: Altogether, this high-resolution analysis of miRNA-target interactions, combining experimental and computational work, Illustrates the close interplay between miRNAs and the response to diverse environmental conditions, in melon. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1679-0) contains supplementary material, which is available to authorized users. BioMed Central 2019-02-18 /pmc/articles/PMC6379984/ /pubmed/30777009 http://dx.doi.org/10.1186/s12870-019-1679-0 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Sanz-Carbonell, Alejandro Marques, María Carmen Bustamante, Antonio Fares, Mario A. Rodrigo, Guillermo Gomez, Gustavo Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon |
title | Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon |
title_full | Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon |
title_fullStr | Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon |
title_full_unstemmed | Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon |
title_short | Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon |
title_sort | inferring the regulatory network of the mirna-mediated response to biotic and abiotic stress in melon |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379984/ https://www.ncbi.nlm.nih.gov/pubmed/30777009 http://dx.doi.org/10.1186/s12870-019-1679-0 |
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