1. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots
- Author
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Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), National Science Foundation (US), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Agencia Estatal de Investigación (España), Álvarez, José Miguel [0000-0002-9826-085X], Moyano, Tomas C. [0000-0001-6495-4995], Gras, D. E. [0009-0000-0874-1995], Araus, Viviana [0000-0001-9457-431X], O'Brien, José Antonio [0000-0002-1788-1786], Carrillo, Laura [0000-0003-2215-322X], Medina, Joaquín [0000-0002-1735-330X], Vicente-Carbajosa, Jesús [0000-0002-6332-1712], Jiang, Jiming [0000-0002-6435-6140], Gutierrez, Rodrigo A. [0000-0002-5961-5005], 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., Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), National Science Foundation (US), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Agencia Estatal de Investigación (España), Álvarez, José Miguel [0000-0002-9826-085X], Moyano, Tomas C. [0000-0001-6495-4995], Gras, D. E. [0009-0000-0874-1995], Araus, Viviana [0000-0001-9457-431X], O'Brien, José Antonio [0000-0002-1788-1786], Carrillo, Laura [0000-0003-2215-322X], Medina, Joaquín [0000-0002-1735-330X], Vicente-Carbajosa, Jesús [0000-0002-6332-1712], Jiang, Jiming [0000-0002-6435-6140], Gutierrez, Rodrigo A. [0000-0002-5961-5005], 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, and Gutierrez, Rodrigo A.
- Abstract
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.
- Published
- 2019