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Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor
BACKGROUND: Identifying the target genes of transcription factors is important for unraveling regulatory networks in all types of organisms. Our interest was precisely to uncover the spectrum of loci regulated by a widespread plant transcription factor involved in physiological adaptation to drought...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923394/ https://www.ncbi.nlm.nih.gov/pubmed/24423251 http://dx.doi.org/10.1186/1471-2229-14-29 |
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author | Ricardi, Martiniano M González, Rodrigo M Zhong, Silin Domínguez, Pía G Duffy, Tomas Turjanski, Pablo G Salgado Salter, Juan D Alleva, Karina Carrari, Fernando Giovannoni, James J Estévez, José M Iusem, Norberto D |
author_facet | Ricardi, Martiniano M González, Rodrigo M Zhong, Silin Domínguez, Pía G Duffy, Tomas Turjanski, Pablo G Salgado Salter, Juan D Alleva, Karina Carrari, Fernando Giovannoni, James J Estévez, José M Iusem, Norberto D |
author_sort | Ricardi, Martiniano M |
collection | PubMed |
description | BACKGROUND: Identifying the target genes of transcription factors is important for unraveling regulatory networks in all types of organisms. Our interest was precisely to uncover the spectrum of loci regulated by a widespread plant transcription factor involved in physiological adaptation to drought, a type of stress that plants have encountered since the colonization of land habitats 400 MYA. The regulator under study, named ASR1, is exclusive to the plant kingdom (albeit absent in Arabidopsis) and known to alleviate the stress caused by restricted water availability. As its target genes are still unknown despite the original cloning of Asr1 cDNA 20 years ago, we examined the tomato genome for specific loci interacting in vivo with this conspicuous protein. RESULTS: We performed ChIP followed by high throughput DNA sequencing (ChIP-seq) on leaves from stressed tomato plants, using a high-quality anti-ASR1 antibody. In this way, we unraveled a novel repertoire of target genes, some of which are clearly involved in the response to drought stress. Many of the ASR1-enriched genomic loci we found encode enzymes involved in cell wall synthesis and remodeling as well as channels implicated in water and solute flux, such as aquaporins. In addition, we were able to determine a robust consensus ASR1-binding DNA motif. CONCLUSIONS: The finding of cell wall synthesis and aquaporin genes as targets of ASR1 is consistent with their suggested role in the physiological adaptation of plants to water loss. The results gain insight into the environmental stress-sensing pathways leading to plant tolerance of drought. |
format | Online Article Text |
id | pubmed-3923394 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-39233942014-02-14 Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor Ricardi, Martiniano M González, Rodrigo M Zhong, Silin Domínguez, Pía G Duffy, Tomas Turjanski, Pablo G Salgado Salter, Juan D Alleva, Karina Carrari, Fernando Giovannoni, James J Estévez, José M Iusem, Norberto D BMC Plant Biol Research Article BACKGROUND: Identifying the target genes of transcription factors is important for unraveling regulatory networks in all types of organisms. Our interest was precisely to uncover the spectrum of loci regulated by a widespread plant transcription factor involved in physiological adaptation to drought, a type of stress that plants have encountered since the colonization of land habitats 400 MYA. The regulator under study, named ASR1, is exclusive to the plant kingdom (albeit absent in Arabidopsis) and known to alleviate the stress caused by restricted water availability. As its target genes are still unknown despite the original cloning of Asr1 cDNA 20 years ago, we examined the tomato genome for specific loci interacting in vivo with this conspicuous protein. RESULTS: We performed ChIP followed by high throughput DNA sequencing (ChIP-seq) on leaves from stressed tomato plants, using a high-quality anti-ASR1 antibody. In this way, we unraveled a novel repertoire of target genes, some of which are clearly involved in the response to drought stress. Many of the ASR1-enriched genomic loci we found encode enzymes involved in cell wall synthesis and remodeling as well as channels implicated in water and solute flux, such as aquaporins. In addition, we were able to determine a robust consensus ASR1-binding DNA motif. CONCLUSIONS: The finding of cell wall synthesis and aquaporin genes as targets of ASR1 is consistent with their suggested role in the physiological adaptation of plants to water loss. The results gain insight into the environmental stress-sensing pathways leading to plant tolerance of drought. BioMed Central 2014-01-14 /pmc/articles/PMC3923394/ /pubmed/24423251 http://dx.doi.org/10.1186/1471-2229-14-29 Text en Copyright © 2014 Ricardi 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. 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 Ricardi, Martiniano M González, Rodrigo M Zhong, Silin Domínguez, Pía G Duffy, Tomas Turjanski, Pablo G Salgado Salter, Juan D Alleva, Karina Carrari, Fernando Giovannoni, James J Estévez, José M Iusem, Norberto D Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor |
title | Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor |
title_full | Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor |
title_fullStr | Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor |
title_full_unstemmed | Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor |
title_short | Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor |
title_sort | genome-wide data (chip-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato asr1, a drought stress-responsive transcription factor |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923394/ https://www.ncbi.nlm.nih.gov/pubmed/24423251 http://dx.doi.org/10.1186/1471-2229-14-29 |
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