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, Gloria M. Coruzzi

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number1157
JournalNature communications
Volume11
Issue number1
DOIs
StatePublished - Dec 1 2020

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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    Alvarez, J. M., Schinke, A. L., Brooks, M. D., Pasquino, A., Leonelli, L., Varala, K., Safi, A., Krouk, G., Krapp, A., & Coruzzi, G. M. (2020). Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade. Nature communications, 11(1), [1157]. https://doi.org/10.1038/s41467-020-14979-6