Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots

Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots

Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.

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Bibliographic Details
Main Authors: Álvarez, José Miguel, Moyano, Tomas C., Zhang, Tao, Gras, D. E., Herrera, Francisco J., Araus, Viviana, O'Brien, José Antonio, Carrillo, Laura, Medina, Joaquín, Vicente-Carbajosa, Jesús, Jiang, Jiming, Gutierrez, Rodrigo A.
Other Authors: Fondo Nacional de Desarrollo Científico y Tecnológico (Chile)
Format: artículo biblioteca
Language:English
Published: Cell Press 2019-12-02
Subjects:RNA polymerase II, Footprinting, Nitrate, Regulatory networks, Transcriptional regulation,
Online Access:http://hdl.handle.net/10261/344272
http://dx.doi.org/10.13039/100000001
http://dx.doi.org/10.13039/501100011033
http://dx.doi.org/10.13039/501100002850
https://api.elsevier.com/content/abstract/scopus_id/85074427941
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Summary:Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.

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