Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions
In: ISSN: 2041-1723, 2019
Online
academicJournal
Zugriff:
International audience ; Charting a temporal path in gene networks requires linking early transcription factor (TF)-triggered events to downstream effects. We scale-up a cell-based TF-perturbation assay to identify direct regulated targets of 33 nitrogen (N)-early response TFs encompassing 88% of N-responsive Arabidopsis genes. We uncover a duality where each TF is an inducer and repressor, and in vitro cis-motifs are typically specific to regulation directionality. Validated TF-targets (71,836) are used to refine precision of a time-inferred root network, connecting 145 N-responsive TFs and 311 targets. These data are used to chart network paths from direct TF 1-regulated targets identified in cells to indirect targets responding only in planta via Network Walking. We uncover network paths from TGA1 and CRF4 to direct TF 2 targets, which in turn regulate 76% and 87% of TF 1 indirect targets in planta, respectively. These results have implications for N-use and the approach can reveal temporal networks for any biological system.
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Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions
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Autor/in / Beteiligte Person: | Brooks, Matthew, D ; Cirrone, Jacopo ; Pasquino, Angelo, V ; Alvarez, José, M ; Swift, Joseph ; Mittal, Shipra ; Juang, Che-Lun ; Varala, Kranthi ; Gutiérrez, Rodrigo, A ; Krouk, Gabriel ; Shasha, Dennis ; Coruzzi, Gloria, M ; Center for Genomics and Systems Biology ; Department of Biology New York ; New York University New York (NYU) ; NYU System (NYU)-NYU System (NYU)-New York University New York (NYU) ; NYU System (NYU)-NYU System (NYU) ; Courant Institute of Mathematical Sciences New York (CIMS) ; Universidad Andrés Bello Santiago (UNAB) ; Purdue University West Lafayette ; Departamento de Genética Molecular y Microbiología (FONDAP) ; Pontificia Universidad Católica de Chile (UC) ; Biochimie et Physiologie Moléculaire des Plantes (BPMP) ; Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) |
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Zeitschrift: | ISSN: 2041-1723, 2019 |
Veröffentlichung: | HAL CCSD ; Nature Publishing Group, 2019 |
Medientyp: | academicJournal |
DOI: | 10.1038/s41467-019-09522-1 |
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