DNA methylation is a conserved epigenetic strategy that enables heritable, yet dynamic, regulation of genome function across eukaryotes, shaping transcriptional outcomes and cellular plasticity. While 5-methylcytosine has long defined the canonical framework of DNA methylation, accumulating evidence reveals N 6 -methyladenine as a regulated DNA modification operating under partially analogous, yet mechanistically distinct, principles. Together with the emerging biological significance of 6mA, recent findings underscore the timeliness of revisiting DNA methylation beyond the 5-methylcytosine paradigm. Recent advances position N 6 -methyladenine as a distinct and complementary DNA methylation system to canonical 5-methylcytosine, reshaping our understanding of eukaryotic genome evolution from a DNA methylation perspective. The lineage-restricted distribution of N 6 -methyladenine further highlights its regulatory machinery as a potentially selective interface for manipulating fungi and unicellular eukaryotes. DNA methylation is a conserved epigenetic strategy that enables heritable, yet dynamic, regulation of genome function across eukaryotes, shaping transcriptional outcomes and cellular plasticity. While 5-methylcytosine has long defined the canonical framework of DNA methylation, accumulating evidence reveals N 6 -methyladenine as a regulated DNA modification operating under partially analogous, yet mechanistically distinct, principles. Together with the emerging biological significance of 6mA, recent findings underscore the timeliness of revisiting DNA methylation beyond the 5-methylcytosine paradigm. Recent advances position N 6 -methyladenine as a distinct and complementary DNA methylation system to canonical 5-methylcytosine, reshaping our understanding of eukaryotic genome evolution from a DNA methylation perspective. The lineage-restricted distribution of N 6 -methyladenine further highlights its regulatory machinery as a potentially selective interface for manipulating fungi and unicellular eukaryotes. DNA methylation events, including 5-methylcytosine (5mC) and N 6 -methyladenine (6mA), represent key epigenetic marks with distinct roles across eukaryotic genomes. Although traditionally viewed as fundamentally divergent, emerging evidence, especially studies on 6mA, reveals striking mechanistic parallels between 5mC and 6mA. In this review, we provide a systematic comparison of the similarities and differences between these two types of DNA methylation, focusing on their genomic distributions, methylation pathways, transcriptional contributions, crosstalk with other epigenetic marks, and evolutionary implications, thereby highlighting their pivotal roles in shaping eukaryotic genomes. By integrating these perspectives, this review emphasizes the fundamental principles shared by these two forms of DNA methylation and offers new insights into their potential roles in eukaryotic evolution.
Nan et al. (Sun,) studied this question.