Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes

Abstract

DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the study of DNA epigenetic modifications has been confined to 5mC and its derivatives for decades. However, rapid developing approaches have witnessed the expansion of DNA modification reservoirs during the past several years, including the identification of 6mA, 5gmC, 4mC, and 4acC in diverse organisms. However, whether these DNA modifications function as epigenetic marks requires careful consideration. In this review, we try to present a panorama of all the DNA epigenetic modifications in eukaryotes, emphasizing recent breakthroughs in the identification of novel DNA modifications. The characterization of their roles in transcriptional regulation as potential epigenetic marks is summarized. More importantly, the pathways for generating or eliminating these DNA modifications, as well as the proteins involved are comprehensively dissected. Furthermore, we briefly discuss the potential challenges and perspectives, which should be taken into account while investigating novel DNA modifications.

Keywords: 5-hydroxymethylcytosine (5hmC); 5-methylcytosine (5mC); DNA demethylation; DNA methylation; DNA modifications; N(6)-methyladenosine (6mA); TET dioxygenases; epigenetic marks; eukaryotes; transcriptional regulation.

Figure 1

Eukaryotic DNA modifications in different nucleotides.A, in mammals, 5mC is generated from cytosines by DNMT, which is subjected to TET-mediated oxidation, resulting in the formation of 5hmC, 5fC, and 5caC. B, 5mC is converted into 5gmC by CMD1 in Chlamydomonas reinhardtii. C, in Bdelloid rotifers, the generation of 4mC is facilitated by N4CMT. D, 4acC, modified by unidentified enzymes, was detected in various plants and mammals. E, in the majority of the Kinetoplastida, the conversion of thymine to 5hmU is attributed to the enzymes JBP1/2. 5hmU is subsequently hypermodified by JGT, resulting in the formation of base J. F, 6mA has been reported to be present in numerous organisms, and the MTA1 complex has been identified as the authentic 6mA methyltransferase in ciliates. 4acC, N⁴-acetyldeoxycytosine; 5caC, 5-carboxylcytosine; 5fC, 5-formylcytosine; 5mC, 5-methylcytosine; 5hmC, 5-hydroxymethylcytosine; 5hmU, 5-hydroxymethyluridine; 6mA, N⁶-methyladenosine; CMD1, 5mC modifying enzyme 1; DNMT, DNA methyltransferase; JBP, J binding protein; JGT, base J–associated glucosyltransferase; MTA1, 6mA methyltransferase; N4CMT, 4mC methyltransferase; TET, ten-eleven translocation.

Figure 2

Active DNA demethylation pathways in plants and mammals. In plants, ROS1 and its homologs cleave 5mC bases, followed by the BER pathway to restore unmodified cytosines, leading to active DNA demethylation. In mammalian cells, TET-mediated DNA oxidation, along with the TDG-initiated BER pathway, constitutes a major pathway in active DNA demethylation. In addition, 5hmC, 5fC, and 5caC might also function as independent epigenetic marks in mammals. 5caC, 5-carboxylcytosine; 5fC, 5-formylcytosine; 5hmC, 5-hydroxymethylcytosine; BER, base excision repair; ROS1, repressor of silencing 1; TDG, thymine DNA glycosylase, TET, ten-eleven translocation.

Figure 3

The schematic diagrams of different TET_JBP domain–containing oxygenases and their enzymatic activities. TET, ten-eleven translocation; JBP, J binding protein.

Figure 4

The multifaceted roles of VC in non-heme iron-dependent oxygenases. VC, vitamin C.

Figure 5

The abundance of 6mA with putative 6mA methyltransferases and demethylases in various species. 6mA, N⁶-methyladenosine.