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

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 investigates how bacterial interactions and environmental factors influence chromatin architecture in Malassezia species using in situ Hi-C. Hi-C libraries were generated under the following conditions: 1) M. restricta co-cultured with S. epidermidis, 2) M. restricta co-cultured with S. aureus, 3) M. restricta cultured under varying pH conditions and in the presence of lactic acid, 4) M. restricta and M. sympodialis treated with acetic acid These datasets provide insights into the three-dimensional genome organization of Malassezia under diverse interkingdom and environmental stimuli, with a focus on epigenetic regulation mediated by microbial metabolites.