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Nat Genet. 2017 Jun;49(6):964-968. doi: 10.1038/ng.3859. Epub 2017 May 8.

Widespread adenine N6-methylation of active genes in fungi.

Author information

1
US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
2
Department of Genetics, University of Georgia, Athens, Georgia, USA.
3
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
4
L. F. Lambert Spawn Co, Coatesville, Pennsylvania, USA.
5
Pacific Northwest National Laboratory, Richland, Washington, USA.
6
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA.
7
Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California, USA.
8
Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, California, USA.
9
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA.
10
School of Natural Sciences, University of California, Merced, Merced, California, USA.

Abstract

N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes, 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. 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-expression-associated epigenomic mark in eukaryotes.

PMID:
28481340
DOI:
10.1038/ng.3859
[Indexed for MEDLINE]
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