Epigenetic Regulation in Early-Diverging Fungi

Epigenetics, defined as the study of heritable change in gene function independent of changes in DNA sequence, offers a fascinating approach to the dynamic regulation of biological processes. Beyond the static information encoded within the genome, epigenetic modifications create a dynamic and intricate layer that regulates gene expression, shaping the phenotypes in response to environmental and endogenous cues. The exploration of epigenetic regulation and its underlying mechanisms has been extensive in animals and plants, incorporating significant contributions from relevant discoveries in yeasts. In addition, studies in asco- and basidiomycetes have also advanced, unveiling several mechanisms primarily dedicated to safeguarding the genome from transposable elements (TEs). However, early-diverging fungi (EDF), which encompass the highest diversity among the fungal kingdom, have received limited attention. We anticipate a forthcoming shift in this scenario, as initial studies have surfaced, and many more are in progress. This transformation is propelled by the accessibility of affordable high-throughput sequencing technologies and the development of new procedures for genome manipulation. This chapter aims to summarize recent discoveries in EDF epigenetics, emphasizing unique features such as the prevalence of 6-methyladenine (6mA) in DNA, a characteristic found at very low levels in most eukaryotes. In addition, we discuss known epigenetics phenomena in EDF, including the control of TEs through RNA interference (RNAi) and constitutive heterochromatin, and the resistance to antifungal drugs by RNAi-dependent generation of epimutants.