PNNL

Abstract

N6-methyldeoxyadenine (6mA) is a non-canonical DNA base modification present at low levels in plant and animal genomes1–4, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging lineages of the fungal kingdom5. Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all adenines were methylated in early-diverging fungi, far exceeding the levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides, was concentrated in dense ‘Methylated Adenine Clusters’ (MACs) surrounding the transcriptional start sites (TSSs) of expressed genes, and its distribution was inversely correlated with 5-methylcytosine (5mC). Our results reveal a striking contrast in the genomic distribution of 6mA and 5mC and reinforce a distinct role of 6mA as a gene expression-associated epigenomic mark in eukaryotes.