Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade.
José M AlvarezAnna-Lena SchinkeMatthew D BrooksAngelo V PasquinoLauriebeth LeonelliKranthi VaralaAlaeddine SafiGabriel KroukAnne KrappGloria M CoruzziPublished in: Nature communications (2020)
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.
Keyphrases
- genome wide
- transcription factor
- dna methylation
- cerebral ischemia
- copy number
- signaling pathway
- gene expression
- subarachnoid hemorrhage
- induced apoptosis
- brain injury
- oxidative stress
- pi k akt
- dna damage
- cell proliferation
- multidrug resistant
- circulating tumor
- cell cycle arrest
- real time pcr
- bioinformatics analysis
- gram negative
- heat shock