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Active histone modifications restrict off-target 6mA deposition and maintain transcriptional stability in Rhizopus microsporus [RNA-seq]

ABSTRACT: 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. Here, we characterize the genome-wide landscape of chromatin organization in 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, the predominant DNA modification in this fungus. We identified functional specialization among Set1 and Gcn5 paralogs, where Set1a primarily deposits H3K4me3, Set1b regulates H3K4me1, and both Gcn5 variants function redundantly in H3K27ac deposition. Knockout analysis reveals that these enzymes are critical for sporulation, stress resistance, and pathogenicity. Importantly, we uncover a hierarchical crosstalk where histone modifications restrict off-target 6mA deposition, regulate methylation cluster stability, and buffer transcriptional variation. Our findings establish R. microsporus as a model for understanding epigenetic compartmentalization in non-dikarya fungi and reveal conserved principles of epigenetic crosstalk that may be fundamental to eukaryotic chromatin regulation.

ORGANISM(S): Rhizopus microsporus

PROVIDER: GSE326211 | GEO | 2026/07/20

REPOSITORIES: GEO

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Active histone modifications restrict off-target 6mA deposition and maintain transcriptional stability in Rhizopus microsporus [ChIP-seq]

Project description: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. Here, we characterize the genome-wide landscape of chromatin organization in 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, the predominant DNA modification in this fungus. We identified functional specialization among Set1 and Gcn5 paralogs, where Set1a primarily deposits H3K4me3, Set1b regulates H3K4me1, and both Gcn5 variants function redundantly in H3K27ac deposition. Knockout analysis reveals that these enzymes are critical for sporulation, stress resistance, and pathogenicity. Importantly, we uncover a hierarchical crosstalk where histone modifications restrict off-target 6mA deposition, regulate methylation cluster stability, and buffer transcriptional variation. Our findings establish R. microsporus as a model for understanding epigenetic compartmentalization in non-dikarya fungi and reveal conserved principles of epigenetic crosstalk that may be fundamental to eukaryotic chromatin regulation.

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