Protocol for analyzing chromatin dynamics in macrophage-internalized Candida glabrata cells using micrococcal nuclease digestion.

Chromatin dynamics plays an important role in medical mycology. Here, we present a protocol to identify nucleosome occupancy and positioning in the fungal pathogen Candida glabrata (Nakaseomyces glabratus). This process involves micrococcal nuclease (MNase) digestion of the chromatin of C. glabrata cells (grown in RPMI medium or inside macrophages), followed by the purification of mononucleosomal DNA fragments. We describe steps for standardizing MNase digestion and identifying genome-wide dynamic nucleosomes using a next-generation sequencing approach. For complete details on the use and execution of this protocol, please refer to Kumar et al.1.