Biology subjects

Tahiri, G.

Publications and source records attributed to Tahiri, G..

5 recordsLinked to original sources

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 Discovery of lncRNAs in Mucorales Reveals Essential Roles in Development and Fungal Biology

Long non-coding RNAs (lncRNAs) emerged as key regulators across eukaryotes, yet their functions in early-diverging fungal (EDF) pathogens remain largely unknown. Here, we provide the first comprehensive identification and characterization of lncRNAs in the EDF order Mucorales, a threatening and WHO high-priority group of opportunistic human pathogens. In this work, we focus on the two major models of this group: Mucor lusitanicus and the clinically relevant pathogen Rhizopus microsporus. We show that EDF lncRNAs exhibit conserved features, dynamic regulation during host interactions, and integration within critical gene regulatory networks. Despite lncRNAs being preferentially encoded in inactive chromatin compartments, we found that their expression is associated with 6mA presence in R. microsporus. Additionally, we also found that lncRNAs can be targeted by both the canonical RNA interference pathway and the non-canonical RNA interference mechanism. Comparative genomics revealed a subset of evolutionarily conserved lncRNAs, including two essential for fungal viability (lncRNA2 and lncRNA4). LncRNA4 disruption, even in heterokaryosis, resulted in severely affected growth and filamentation. These results establish lncRNAs as indispensable regulators of fungal physiology and pathogenicity, highlighting their potential as novel antifungal targets.

genetics↗

bioRxiv2025

A BRCT Domain-Containing Protein Induced in Early Phagocytosis Plays a Crucial Role in Mucorales Pathogenesis

Mucormycosis, caused by Mucoralean fungi, is among the most lethal fungal diseases, and a deeper understanding of its pathogenesis is urgently needed. Transcriptomic profiling of virulent (WT) and an RNAi-deficient strain (r3b2{Delta}) of M. lusitanicus strains during phagocytosis uncovered thousands of differentially expressed genes (DEGs), highlighting early metabolic activation as a key survival strategy inside the phagosome. Enriched pathways included amino acid transport, nucleotide metabolism, and translation, reflecting an adaptive fungal response to nutrient deprivation and host immune stress. Integrative analyses of mRNA and sRNA profiles also revealed a critical role of the RNAi pathways in modulating gene expression during infection.Building on these observations, we identified four chromatin- and transcription-related candidate virulence genes--brca1, box, hist1, and hda10--which were strongly upregulated during phagocytosis and regulated by RNAi. Functional validation through gene deletion in M. lusitanicus and disruption in R. microsporus revealed that while loss of these genes in M. lusitanicus did not significantly affect virulence, R. microsporus mutants for brca1, hist1, and hda10 showed attenuated virulence in a murine model. Our findings suggest that although M. lusitanicus remains a valuable tool for genetic manipulation, species-specific differences must be considered when studying virulence. The study also underscores the importance of using multiple Mucorales models to uncover conserved and divergent strategies employed by pathogenic fungi. These insights contribute to a broader understanding of fungal adaptation, immune evasion, and the identification of novel targets for antifungal intervention.

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↗

bioRxiv2023

H3K4 methylation regulates development, DNA repair, and virulence in Mucorales

Mucorales are basal fungi that opportunistically cause a fatal infection known as mucormycosis (black fungus disease), which poses a significant threat to human health due to its high mortality rate and its recent association with SARS-CoV-2 infections. On the other hand, histone methylation is a regulatory mechanism with pleiotropic effects, including the virulence of several pathogenic organisms. However, the role of epigenetic changes at the histone level never has been studied in Mucorales. Here, we dissected the functional role of Set1, a histone methyltransferase that catalyzes the methylation of H3K4, which is associated with the activation of gene transcription and virulence. A comparative analysis of the Mucor lusitanicus genome (previously known as Mucor circinelloides f. lusitanicus) identified only one homolog of Set1 from Candida albicans and Saccharomyces cerevisiae that contains the typical SET domain. Knockout strains in the gene set1 lacked H3K4 monomethylation, dimethylation, and trimethylation enzymatic activities. These strains also showed a significant reduction in vegetative growth and sporulation. Additionally, set1 null strains were more sensitive to SDS, EMS, and UV light, indicating severe impairment in the repair process of the cell wall and DNA lesions and a correlation between Set1 and these processes. During pathogen-host interactions, strains lacking the set1 gene exhibited shortened polar growth within the phagosome and attenuated virulence both in vitro and in vivo. Our findings suggest that the histone methyltransferase Set1 coordinates several cell processes related to the pathogenesis of M. lusitanicus and may be an important target for future therapeutic strategies against mucormycosis. Author SummaryThe knowledge regarding the role of epigenetic modification in regulating gene expression in early diverging fungi is scarce, despite they represent an important fraction of the fungal kingdom. The order Mucorales, which causes the lethal infection known as mucormycosis, is not an exception. There is an urgent need to enhance our understanding of the biology of these fungi to develop effective treatments for mucormycosis, which are currently absent due to the natural resistance of Mucorales to most antifungal drugs. This work represents the first investigation into the role of the methylation of lysine 4 on histone 3 (H3K4) in a mucoralean fungus. This was accomplished by the generation of deletion mutants in the set1 gene, which encodes the specific H3K4 methyltransferase. Phenotypic analyses of these mutants suggest that H3K4 methylation regulates physiology, development, cell wall integrity, and DNA repair. Furthermore, our findings indicate that it also contributes to the virulence of M. lusitanicus, as strains lacking the set1 gene exhibited shortened polar growth within the phagosome and attenuated virulence both in vitro and in vivo.

genetics↗