Isw2-dependent chromatin remodeling at the CRZ1 promoter governs azole tolerance in Candida albicans

Here, we conducted a quantitative analysis of transcription factor deletion mutants in Candida albicans to identify novel modulators of azole tolerance. We found that loss of ISW2, which encodes the catalytic subunit of an ATP-dependent chromatin-remodeling complex, markedly increased azole tolerance, establishing Isw2 as a negative regulator of this phenotype in C. albicans. By integrating RNA-seq and ChEC-seq analyses, we defined the Isw2 regulon and discovered that this remodeler binds and modulates nucleosome dynamics at the promoter of CRZ1, a transcription factor that acts downstream of the calcineurin pathway and is a key regulator of azole tolerance. Consistent with this, CRZ1 transcript levels were elevated in the isw2 mutant, supporting a model in which Isw2 modulates antifungal tolerance by directly restricting CRZ1 transcription. Overall design: In this study, we identified transcripts that were differentially regulated in the isw2 mutant, which lacks the chromatin remodeler Isw2. The transcriptional profile of isw2 cells grown in the synthetic complete medium supplemented or not with the antifungal amphotericin B (0.45 µg/ml) was compared to that of the wild-type (WT) strain grown under the same conditions. For ChEC-seq, DNA cleavage profiles from Isw2-MNase cells (C-terminal MNase-tagged ISW2 at the native locus) were normalized to those from MNase-free control cells (WT cells with ectopic MNase expression).