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

Author

Listed:
  • José M. Alvarez

    (New York University
    Universidad Mayor)

  • 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)

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.

Suggested Citation

  • José M. Alvarez & Anna-Lena Schinke & Matthew D. Brooks & Angelo Pasquino & Lauriebeth Leonelli & Kranthi Varala & Alaeddine Safi & Gabriel Krouk & Anne Krapp & Gloria M. Coruzzi, 2020. "Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-14979-6
    DOI: 10.1038/s41467-020-14979-6
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    Cited by:

    1. Sanghwa Lee & Julia Showalter & Ling Zhang & Gaëlle Cassin-Ross & Hatem Rouached & Wolfgang Busch, 2024. "Nutrient levels control root growth responses to high ambient temperature in plants," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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