Crosstalk between the Ino80 complex and TOR signaling drives fungal adaptation to hypoxia through chromatin remodeling

In the present study, we undertook a genetic screen of the GRACE (Gene Replacement and Conditional Expression) collection to identify genes required for hypoxic (5% O2) adaptation. Through this comprehensive screen, we identified many genes spanning diverse functional categories that are required for optimal growth under hypoxia, revealing new pathways likely involved in O2 sensing, signaling, and adaptation to O2 depletion. We identified two subunits of the Ino80 chromatin-remodeling complex and one subunit of the TOR (Target Of Rapamycin) pathway as critical for sustaining fungal growth under O2-depleted conditions. Integration of ino80 mutant transcriptomic data with Ino80 DNA-binding and nucleosome-occupancy profiles under conditional INO80 depletion revealed that this chromatin remodeler controls the cellular phosphate demand accompanying hypoxic adaptation. The similarity between chromatin accessibility changes upon TOR inhibition and INO80 depletion suggests that Ino80 functions in concert with the TOR pathway to promote growth and maintain phosphate homeostasis under O2-limiting conditions. These findings provide new insight into how nutrient and O2 signaling converge on chromatin remodeling mechanisms, offering a foundation for understanding the regulatory logic that underlies hypoxic adaptation in pathogenic fungi. Overall design: In this study, we identified transcripts that were differentially regulated in the ino80 mutant, which lacks the chromatin remodeler Ino80. The transcriptional profile of ino80 cells grown under hypoxic conditions (5% O2) was compared to that of the wild-type (WT) strain grown under the same conditions. Hypoxia-responsive genes were determined by comparing the transcriptome of WT cells grown under hypoxia (5% O2) to that of cells maintained under normoxia (21% O2). For ChEC-seq, DNA cleavage profiles from Ino80-MNase cells (C-terminal MNase-tagged INO80 at the native locus) were normalized to those from MNase-free control cells (WT cells with ectopic MNase expression). For MNase-seq, DNA counts from doxycycline-treated pTET-INO80 or pTET-TOR1 strains (INO80- and TOR1-depleted cells) were compared to those of their untreated counterparts.