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.
