Nicolas-Munoz, N. | Search bioRxiv

bioRxiv2026

Active histone modifications fine-tune DNA N-6 methyladenine deposition and maintain transcriptional stability

Epigenetic mechanisms provide sophisticated regulatory layers that modulate gene expression across diverse organisms, yet their organization and crosstalk remain poorly understood in non-dikarya fungi (NDF). Here, we characterize the genome-wide landscape of chromatin organization in the fungus Rhizopus microsporus, revealing a compartmentalized architecture where active histone modifications (H3K4me1, H3K4me3, H3K27ac) define transcriptionally active euchromatin distinct from H3K9me3-marked constitutive heterochromatin. Through comprehensive ChIP-seq analysis, we demonstrate that these modifications exhibit distinct distribution patterns over gene bodies and co-localize with 6-methyladenine (6mA) clusters (MACs), an essential epigenetic mark that is associated with transcription in this fungus. We identified functional specialization among H3K4 methyltransferase Set1 paralogs, where Set1a primarily deposits H3K4me3 and Set1b deposits H3K4me1. In contrast, both Gcn5 paralogs function redundantly in H3K27 acetylation. Knockout analysis reveals that these enzymes are critical for sporulation, stress resistance, and pathogenesis. Importantly, we uncover an epigenetic crosstalk in which active histone modifications restrict off-target 6mA deposition, regulate methylation cluster stability, and buffer transcriptional variation. Our findings reveal conserved principles of epigenetic crosstalk between active histone modifications and the essential DNA modification 6mA that may represent a fundamental mechanism of chromatin regulation in eukaryotes. SIGNIFICANCEEpigenetic mechanisms regulate gene activity without altering the DNA sequence, yet how different epigenetic marks interact remains poorly understood. Here, we characterize the genome-wide distribution of active histone modifications and DNA N6-methyladenine (6mA) in the fungus Rhizopus microsporus, revealing that they define distinct active and inactive chromatin domains. While 6mA plays a central role in transcriptional regulation, active histone modifications direct its accurate deposition and maintenance, thereby reducing transcriptional variability. These findings uncover conserved crosstalk between histone modifications and 6mA that may represent a fundamental principle of chromatin regulation across eukaryotes.

genetics↗

bioRxiv2025

Genome-wide exploration of the transcriptional regulatory landscape in the early-diverging fungus R. microsporus reveals pervasive DNA methyl adenine regulatory network

Genetic regulation mechanisms rely on complex transcriptional networks that are often difficult to decipher. The study of transcription factor (TF) binding sites and their targets has traditionally faced scalability challenges, hindering comprehensive cistrome analyses. However, the development of the DNA affinity purification and sequencing (DAP-seq) technique has allowed unprecedented large-scale studies at genome-wide level of TF binding with high reproducibility. In this study, we apply this technique to the human opportunistic pathogen R. microsporus, a mucoralean fungus belonging to the understudied group of early-diverging fungi (EDF). We characterize genome-wide binding sites of 58 TFs encoded by genes regulated through adenine methylation and representing major TF families, representing the most extensive DAP-seq study in filamentous fungi. This analysis reveals their binding profiles and recognized sequences, expanding and diversifying the catalog of known fungal motifs. By integrating this data with DNA 6-methyladenine profiling, we uncover the extensive direct and indirect impact of this epigenetic modification on the regulation of gene expression. Furthermore, the generated data facilitates the identification and functional characterization of TFs involved in biologically relevant processes, such as zinc metabolism and light response, serving as a proof of concept for the utility of the DAP-seq data. These findings not only enhance our understanding of regulatory mechanisms in R. microsporus but also provide broader insights into gene regulation across the fungal kingdom.

genetics↗