Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns

DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation...

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Published inFrontiers in microbiology Vol. 11; p. 616922
Main Authors Nai, Yu-Shin, Huang, Yu-Chun, Yen, Ming-Ren, Chen, Pao-Yang
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 22.01.2021
Subjects
DNA methylation
DNA methyltransferases
DNMT5
epigenomics
fungi
Microbiology
transposable element
DNA methylation
epigenomics
DNA methyltransferases
fungi
DNMT5
transposable element
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Summary:DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation profiles were found to be very diverse and have gained many research interests. We reviewed fungal DNMTs in terms of their biological functions, protein domain structures, and their associated epigenetic regulations compared to those known in plant and animal systems. In addition, we summarized recent reports on potential RNA-directed DNA methylation (RdDM) related to DNMT5 in fungi. We surveyed up to 40 fungal species with published genome-wide DNA methylation profiles (methylomes) and presented the associations between the specific patterns of fungal DNA methylation and their DNMTs based on a phylogenetic tree of protein domain structures. For example, the main DNMTs in Basidiomycota, DNMT1 with RFD domain + DNMT5, contributing to CG methylation preference, were distinct from RID + Dim-2 in Ascomycota, resulting in a non-CG methylation preference. Lastly, we revealed that the dynamic methylation involved in fungal life stage changes was particularly low in mycelium and DNA methylation was preferentially located in transposable elements (TEs). This review comprehensively discussed fungal DNMTs and methylomes and their connection with fungal development and taxonomy to present the diverse usages of DNA methylation in fungal genomes.
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Reviewed by: Jiamu Du, Southern University of Science and Technology, China; Siew Pheng Lim, Denka Life Innovation Research (DLIR), Singapore; Stefan Kusch, RWTH Aachen University, Germany; Jiangzhao Qian, RWTH Aachen University, Aachen, Germany, in collaboration with reviewer SK
These authors have contributed equally to this work
Edited by: Junbiao Dai, Chinese Academy of Sciences (CAS), China
This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology
ISSN:1664-302X
1664-302X
DOI:10.3389/fmicb.2020.616922