Journal
MOLECULAR PLANT
Volume 12, Issue 12, Pages 1545-1560Publisher
CELL PRESS
DOI: 10.1016/j.molp.2019.09.002
Keywords
nitrate; transcriptional regulation; footprinting; RNA polymerase II; regulatory networks
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Funding
- Instituto Milenio iBio - Iniciativa Cientifica Milenio MINECON, Chile
- Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation, Chile [15090007]
- Fondo Nacional de Desarrollo Cientifico y Tecnologico (FONDECYT), Chile [1180759]
- FONDECYT, Chile [3140336]
- National Science Foundation, United States [MCB-1412948]
- Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Spain [RTA2015-00014-c02-01]
- Severo Ochoa Program for Centers of Excellence in R&D from the Agencia Estatal de Investigacion of Spain [SEV-2016-0672]
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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 m RNA 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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