Abstract
Human fungal pathogens often encounter fungicidal stress upon host invasion, but they can swiftly adapt by transcriptional reprogramming that enables pathogen survival. Fungal immune evasion is tightly connected to chromatin regulation. Hence, fungal chromatin modifiers pose alternative treatment options to combat fungal infections. Here, we present an assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol adapted for the opportunistic pathogen Candida albicans to gain further insight into the interplay of chromatin accessibility and gene expression mounted during fungal adaptation to oxidative stress. The ATAC-seq workflow not only facilitates the robust detection of genomic regions with accessible chromatin but also allows for the precise modeling of nucleosome positions in C. albicans. Importantly, the data reveal genes with altered chromatin accessibility in upstream regulatory regions, which correlate with transcriptional regulation during oxidative stress. Interestingly, many genes show increased chromatin accessibility without change in gene expression upon stress exposure. Such chromatin signatures could predict yet unknown regulatory factors under highly dynamic transcriptional control. Additionally, de novo motif analysis in genomic regions with increased chromatin accessibility upon H2O2 treatment shows significant enrichment for Cap1 binding sites, a major factor of oxidative stress responses in C. albicans. Taken together, the ATAC-seq workflow enables the identification of chromatin signatures and highlights the dynamics of regulatory mechanisms mediating environmental adaptation of C. albicans.
Highlights
Human fungal pathogens respond to host immune defense through numerous mechanisms, including chromatin-mediated adaptive gene expression [1,2,3]
We demonstrate that H2 O2 -treated (H2 O2) -treatment of fungal cells increases chromatin accessibility in upstream regions of genes associated with the oxidative response, and we show that those genes tend to be transcriptionally upregulated
(gDNA) prepared from YPD-grown C. albicans was included in the workflow (Figure 1A; see Materials and Methods for details)
Summary
Human fungal pathogens respond to host immune defense through numerous mechanisms, including chromatin-mediated adaptive gene expression [1,2,3]. Immune defense or environmental changes can trigger pathogen responses through extracellular sensing, intracellular signal transduction, and transcriptional reprogramming [4,5]. Transcriptional changes require a tight interplay of chromatin states and transcription factors [6,7], as the swift adaptation to environmental changes is often paramount for a successful lifestyle or immune evasion. Pathogens encounter a number of extreme stress conditions during the course of an infection. These include limitations in nutrient availability and the cytotoxic attack by the host immune system [8,9]. C. albicans lives as a harmless commensal in the majority of humans, colonizing mucosal surfaces and epithelial barriers, especially the intestinal tract
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