Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus

Carlos Lax, Leo A. Baumgart, Ghizlane Tahiri, Natalia Nicolás-Muñoz, Yu Zhang, Ian K. Blaby, Stephen J. Mondo, Bishoy Kamel, Ronan C. O’Malley, Vivian Ng, Eusebio Navarro, Igor V. Grigoriev, Francisco E. Nicolás () and Victoriano Garre ()
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Carlos Lax: Universidad de Murcia, Departamento de Genética y Microbiología, Facultad de Biología
Leo A. Baumgart: Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute
Ghizlane Tahiri: Universidad de Murcia, Departamento de Genética y Microbiología, Facultad de Biología
Natalia Nicolás-Muñoz: Universidad de Murcia, Departamento de Genética y Microbiología, Facultad de Biología
Yu Zhang: Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute
Ian K. Blaby: Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute
Stephen J. Mondo: Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute
Bishoy Kamel: Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute
Ronan C. O’Malley: University of Chicago, Department of Human Genetics
Vivian Ng: Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute
Eusebio Navarro: Universidad de Murcia, Departamento de Genética y Microbiología, Facultad de Biología
Igor V. Grigoriev: Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute
Francisco E. Nicolás: Universidad de Murcia, Departamento de Genética y Microbiología, Facultad de Biología
Victoriano Garre: Universidad de Murcia, Departamento de Genética y Microbiología, Facultad de Biología

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Development of the DNA affinity purification and sequencing (DAP-seq) technique has allowed genome-scale studies of transcription factor (TF)-binding sites with high reproducibility. Here, we apply this technique to the human opportunistic pathogen Rhizopus microsporus, a mucoralean fungus belonging to the understudied group of early-diverging fungi. We characterize genome-wide binding sites of 58 TFs encoded by genes regulated through adenine methylation and representing major TF families. 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, we use the generated data to identify TFs involved in biologically relevant processes such as zinc metabolism and light response. Our work enhances our understanding of regulatory mechanisms in R. microsporus and provides broader insights into gene regulation across the fungal kingdom.

Date: 2025
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DOI: 10.1038/s41467-025-65177-1

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