P-274 - Exploring the Impact of DNA Methylation on three-dimensional genome architecture in a major wheat pathogen

Genome structure and maintenance are key determinants of the evolvability of organisms. In eukaryotes, including fungi, genomes are organized within three-dimensional (3D) nuclear space, where chromosomes occupy distinct regions. The genome of the wheat pathogen Zymoseptoria tritici is partitioned into gene-rich, transposon-poor core compartments and accessory compartments enriched in species-specific genes and transposable elements (TEs). We recently uncovered the 3D conformation of the Z. tritici reference genome, revealing topologically associating domain (TAD)-like structures associated with distinct epigenetic and transcriptomic landscapes. Notably, TAD-like boundary regions were enriched in specific histone modifications, depleted in cytosine DNA methylation, and showed low TE content. Cytosine DNA methylation plays a critical role in silencing TEs and maintaining genome integrity. In natural populations of Z. tritici, the loss of the DNA methyltransferase DIM2 led to a nearly complete loss of cytosine DNA methylation, resulting in TE reactivation. However, the influence of DNA methylation variation on 3D genome conformation remains poorly understood. In this study, we combined Hi-C, genome, transcriptome, and methylome sequencing of two pairs of Z. tritici strains with active and inactive DIM2 to investigate how variation in DNA methylation affects genome architecture and 3D organization.