Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade

José M. Alvarez, Anna-Lena Schinke, Matthew D. Brooks, Angelo Pasquino, Lauriebeth Leonelli, Kranthi Varala, Alaeddine Safi, Gabriel Krouk, Anne Krapp and Gloria M. Coruzzi ()
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José M. Alvarez: New York University
Anna-Lena Schinke: New York University
Matthew D. Brooks: New York University
Angelo Pasquino: New York University
Lauriebeth Leonelli: New York University
Kranthi Varala: Purdue University
Alaeddine Safi: BPMP, Université de Montpellier, CNRS, INRA, SupAgro
Gabriel Krouk: BPMP, Université de Montpellier, CNRS, INRA, SupAgro
Anne Krapp: Université Paris-Saclay
Gloria M. Coruzzi: New York University

Nature Communications, 2020, vol. 11, issue 1, 1-13

Abstract: Abstract Dynamic reprogramming of gene regulatory networks (GRNs) enables organisms to rapidly respond to environmental perturbation. However, the underlying transient interactions between transcription factors (TFs) and genome-wide targets typically elude biochemical detection. Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-series chromatin immunoprecipitation (ChIP-seq) and/or DNA adenine methyltransferase identification (DamID-seq). The transient TF-target interactions captured uncover the early mode-of-action of NIN-LIKE PROTEIN 7 (NLP7), a master regulator of the nitrogen signaling pathway in plants. These transient NLP7 targets captured in root cells using temporal TF perturbation account for 50% of NLP7-regulated genes not detectably bound by NLP7 in planta. Rapid and transient NLP7 binding activates early nitrogen response TFs, which we validate to amplify the NLP7-initiated transcriptional cascade. Our approaches to capture transient TF-target interactions genome-wide can be applied to validate dynamic GRN models for any pathway or organism of interest.

Date: 2020
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DOI: 10.1038/s41467-020-14979-6

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