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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

Martiniano M Ricardi1, Rodrigo M González1, Silin Zhong2, Pía G Domínguez3, Tomas Duffy3, Pablo G Turjanski4, Juan D Salgado Salter1, Karina Alleva5, Fernando Carrari3, James J Giovannoni6, José M Estévez1 and Norberto D Iusem17*

Author Affiliations

1 Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE)-CONICET, Buenos Aires, Argentina

2 Boyce Thompson Institute for Plant Research, Tower Road, Cornell University, Ithaca, NY, USA

3 Instituto de Biotecnología – INTA, Hurlingham, Provincia de Buenos Aires, Argentina

4 Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina

5 Instituto de Biodiversidad y Biología Experimental (IBBEA, CONICET-UBA), Buenos Aires, Argentina

6 Department of Plant Biology, Cornell University, Ithaca, NY, USA

7 Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina

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BMC Plant Biology 2014, 14:29  doi:10.1186/1471-2229-14-29

Published: 14 January 2014



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.


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.


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.

Tomato; ASR1; ChIP-seq; Water stress; Cell wall; Aquaporin