PHYTOCHROME INTERACTING FACTORs trigger environmentally responsive chromatin dynamics

The pivotal interplay between light receptors and PHYTOCHROME-INTERACTING FACTORs (PIFs) serves as an essential regulatory hub that perceives and integrates environmental cues into the plant’s transcriptional networks. A critical control component of environmentally-responsive gene networks is the histone variant H2A.Z which provides transcriptional plasticity and prevents undesired gene activation. However, the functional relationship between PIF transcription factors (TFs) and H2A.Z is despite their outstanding importance, only poorly understood. Here, we describe a photo-genomic approach that utilizes the rapid and reversible light-mediated manipulation of PIF7 activity to visualize PIF7 DNA binding and H2A.Z occupancy kinetics on a genome-wide scale. Strikingly, we discovered that PIF shape the H2A.Z landscape in a light quality-dependent manner. We found that DNA binding of PIF7 is not regulated by H2A.Z but most importantly, PIFs initiate H2A.Z eviction and through the direct interaction with EIN6 ENHANCER (EEN), a crucial subunit of INO80 chromatin remodeling complex. Collectively, we describe a PIF-INO80 regulatory module that controls plant growth in response to environmental changes. ChIP-seq and RNA-seq was applied to comprehensively profile the H2A.Z landscape in response to low R:FR light exposure