Widespread adenine N6-methylation of active genes in fungi

Abstract

N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes 1-4 , 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 fungal lineages 5 . 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 levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expressionassociated epigenomic mark in eukaryotes.

SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis

“…Twenty-eight 4mC (0.13%) and 10 6mA (0.017%) modification sites were identified in the O. sinensis mt genome ( Figure 1 and Table 6 ). The 6mA levels were lower than previously reported for nucleotide methylation (0.048–0.21%) in eukaryotic nuclear genomes (Mondo et al, 2017). Most 6mA and 4mC were distributed in intergenic regions (between tRNA and nad4L / nad6/cox2 , or between tRNA and tRNA) or in intron regions of different genes (e.g., nad1 - 2, cox1 - 2, cob, rnl ), with only three located in the genes.…”

“…Bisulfite sequencing has enabled genome-wide surveys of 5mC methylation (Masser et al, 2016), a well-established epigenomic mark in eukaryotes, but the historic absence of tools for studying 6mA and 4mC modifications has precluded more comprehensive studies of 6mA and 4mC methylation. Recently, Mondo et al (2017) firstly analyzed 6mA in fungi by SMRT, and revealed its role as a gene-expression-associated epigenomic mark. In this study, SMRT sequencing revealed that not only 6mA but also 4mC were presented in the fungal mt genome.…”

A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi

“…Genes for the enzymes that modify DNA or histones are also largely conserved [14, 18, 26]. One recent major discovery is the rather widespread distribution of 6-methyladenine observed in the basal lineages that is apparently absent from the Dikarya [30]. Similarly, the Sacharomycetaceae can no longer methylate cytosines or adenines in DNA or methylate lysines of histone H3 at positions 9 and 27 (Figure 1).…”

Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing

“…2–4 Another naturally occurring DNA modification, N 6 -methyladenine ( N 6 -mA or 6mA) (Figure 1a), was previously thought to be absent in metazoans and only present in prokaryotes and a limited number of unicellular eukaryotes. 5,6 Recently, several new reports described the genomic distributions of N 6 -mA in many phylogenetically distinct eukaryotes including fungi, 7 green algae, 8 insects, 9 nematodes, 10 frogs, 11 fish, 12 and mammals. 11–13 Interestingly, the genomic abundance of N 6 -mA varies from ~0.0001–0.0003% of adenines in plants and mammals to as high as 2.8% of adenines in early diverging fungi.…”