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. Ricardi, Rodrigo M. González, Silin Zhong, Pía G. Domínguez, Tomas Duffy, Pablo G. Turjanski, Juan D. Salgado Salter, Karina Alleva, Fernando Carrari, James J. Giovannoni, José M. Estévez, Norberto D. Iusem

Resultado de la investigación: Article

42 Citas (Scopus)

Resumen

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.

Idioma originalEnglish
Número de artículo29
PublicaciónBMC Plant Biology
Volumen14
N.º1
DOI
EstadoPublished - 14 ene 2014

Huella dactilar

aquaporins
water stress
transcription factors
cell walls
tomatoes
genome
loci
genes
synthesis
DNA-binding domains
plant adaptation
water
plant stress
drought tolerance
solutes
molecular cloning
drought
Arabidopsis
genomics
antibodies

ASJC Scopus subject areas

  • Plant Science

Citar esto

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. En: BMC Plant Biology. 2014 ; Vol. 14, N.º 1.
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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",
abstract = "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.",
keywords = "Aquaporin, ASR1, Cell wall, ChIP-seq, Tomato, Water stress",
author = "Ricardi, {Martiniano M.} and Gonz{\'a}lez, {Rodrigo M.} and Silin Zhong and Dom{\'i}nguez, {P{\'i}a G.} and Tomas Duffy and Turjanski, {Pablo G.} and {Salgado Salter}, {Juan D.} and Karina Alleva and Fernando Carrari and Giovannoni, {James J.} and Est{\'e}vez, {Jos{\'e} M.} and Iusem, {Norberto D.}",
year = "2014",
month = "1",
day = "14",
doi = "10.1186/1471-2229-14-29",
language = "English",
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journal = "BMC Plant Biology",
issn = "1471-2229",
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Ricardi, MM, González, RM, Zhong, S, Domínguez, PG, Duffy, T, Turjanski, PG, Salgado Salter, JD, Alleva, K, Carrari, F, Giovannoni, JJ, Estévez, JM & Iusem, ND 2014, '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', BMC Plant Biology, vol. 14, n.º 1, 29. https://doi.org/10.1186/1471-2229-14-29

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.

En: BMC Plant Biology, Vol. 14, N.º 1, 29, 14.01.2014.

Resultado de la investigación: Article

TY - JOUR

T1 - 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

AU - Ricardi, Martiniano M.

AU - González, Rodrigo M.

AU - Zhong, Silin

AU - Domínguez, Pía G.

AU - Duffy, Tomas

AU - Turjanski, Pablo G.

AU - Salgado Salter, Juan D.

AU - Alleva, Karina

AU - Carrari, Fernando

AU - Giovannoni, James J.

AU - Estévez, José M.

AU - Iusem, Norberto D.

PY - 2014/1/14

Y1 - 2014/1/14

N2 - 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.

AB - 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.

KW - Aquaporin

KW - ASR1

KW - Cell wall

KW - ChIP-seq

KW - Tomato

KW - Water stress

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U2 - 10.1186/1471-2229-14-29

DO - 10.1186/1471-2229-14-29

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C2 - 24423251

AN - SCOPUS:84892393715

VL - 14

JO - BMC Plant Biology

JF - BMC Plant Biology

SN - 1471-2229

IS - 1

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ER -