Acetic acid produced by Staphylococcus epidermidis remodels chromatin architecture and suppresses gene expression in Malassezia restricta [RNA-Seq]

Malassezia restricta and Staphylococcus epidermidis are dominant members of the human skin microbiome that interact closely, yet the molecular basis of their interaction remains unclear. In this study, we investigated how S. epidermidis-derived acetic acid (AcOH) influences chromatin organization in M. restricta. We generated the first high-resolution three-dimensional genome architecture map of M. restricta using in situ Hi-C and identified putative centromeric regions based on inter-chromosomal contact patterns. Exposure to AcOH, either by co-culture or direct treatment, led to large-scale chromatin decompaction and enhanced centromere clustering. These findings indicate that AcOH acts as an epigenetic modulator, inducing significant reorganization of nuclear architecture in M. restricta. This dataset provides a resource for understanding interkingdom interactions and the epigenetic effects of bacterial metabolites on fungal chromatin structure. This study explores how organic acid exposure and pH changes affect gene expression in M. restricta. RNA-Seq libraries were generated under the following conditions: 1) M. restricta cultured under normal conditions (untreated control), 2) M. restricta treated with HCl to adjust the medium to pH 5.0, 3) M. restricta treated with acetic acid to adjust the medium to pH 5.0. These datasets provide insights into the transcriptional responses of M. restricta to acidic stress by HCl and acetic acid.