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

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.