Chromatin accessibility contributes to Candida albicans adaptation to echinocandins

Infections by the major opportunistic pathogen of human Candida albicans are commonly treated with echinocandin (ECN) drugs. However, C. albicans can adapt to grow in the presence of certain amounts of ECNs. Prior studies by several laboratories have defined multiple genes, as well as mechanisms involving induced aneuploidy, that can govern this. Still, mechanisms of ECN adaptation are not fully understood. Here, we use genome-wide profiling of chromatin accessibility by ATAC-seq to determine if ECN adaptation is reflected in changes in the chromatin landscape in the absence of aneuploidy. We find that drug adaptation is coupled with multiple changes in chromatin accessibility genome-wide, which occur predominantly in gene promoter regions. Areas of increased accessibilities in promoters are enriched with the binding motifs for at least two types of transcription factors: zipfinger and b-zipfinger. We also find that chromatin changes are often associated with differentially-expressed genes including genes with functions relevant to the ECN-adapted phenotype, such as cell wall biosynthesis. Consistent with this, we find that the cell wall is remodeled in ECN-adapted mutants, with chitin up and glucan down and increased cell surface exposure. Full understanding of ECN adaptation processes is of critical importance for prevention of clinical resistance. Overall design: Three independent batches of C. albicans grown in YPD were used for nuclei preparation based on published protocol with minor modifications (Jenull et al., 2020). Tagmentation done as in (Jenull et al., 2020.). JMC200-2-5 and JMC160-2-5 are caspofungin adapted mutants whereas Parental (JRCT1) samples were used as control samples. gDNA control was used as tagmentation and background control.