ANTAGONISTIC RELATION BETWEEN DNA METHYLATION AND DNA REPLICATION: A STUDY ON ZEBRAFISH

 

Cell phenotype stability in developing organisms is based on error-free transmission of genetic and epigenetic information on mitosis. Cytosine residues of genomic DNA are methylated, marking as a key epigenetic modulation that regulates gene expression and prevents genome instability. On replication of the DNA template in S phase of cell cycle, specific DNA methylation patterns for types of cells are copied from the parental strand to the daughter strand due to maintenance methylase Dnmt1 (DNA methyltransferase 1,  an enzyme that transfers methyl groups to specific CpG structures in DNA.) along with a contribution by de novo methylases Dnmt3a and Dnmt3b, responsible for establishing DNA methylation patterns during embryogenesis and germ cell development. Generally, methylated cytosine mostly takes place in CG dinucleotides, alternatively, in certain types of cells like mouse germinal vesicular oocytes, non-CG sites (referred to as CH) are noted to be heavily methylated.

Methylation patterns at the palindromic CG site are restored or transferred in a biphasic pattern in parental DNA. In the first phase, Dnmt1 works on the already partially methylated region in the new strand through the replication fork. Dnmt1 prefers to work on specific sites in the DNA called CG sites, especially those that are partially methylated during replication, it has less activity on the non-CG sites. On the other hand, in the second phase of restoration, Dnmt3a and Dnmt3b play a major role. The second phase of restoration happens independently of DNA replication and continues throughout the cell cycle. Dnmt1 is not directly connected to the DNA copying process in this phase.  Dnmt3a and Dnmt3b have de novo methylation activity, which methylates partially (CHG) or non-palindromic (CHH) sites (H representing A, C, or T). This intricate interplay between different DNA methyltransferases highlights the complexity of epigenetic regulation and the varied preferences of these enzymes for distinct sequence contexts.

A recent paper “Antagonistic interactions safeguard mitotic propagation of genetic and epigenetic information in zebrafish” published in Communication Biology of Nature suggests an interesting relationship between the inhibition of DNA replication (synthesis) and the heightened activity of enzymes responsible for adding new methyl groups to DNA.

Observably, in the treatment of cells with DNA synthesis inhibitors, DNA hypermethylation (increased addition of methyl groups to DNA) is linked which is mediated by de novo enzyme activity. This observation strengthens the idea that there is an inverse relationship between DNA replication and the maintenance of DNA methylation. In simpler terms, when DNA replication is slowed down or inhibited, the processes that maintain DNA methylation seem to become more active, leading to an increase in overall DNA methylation levels. To address potential limitations associated with studies conducted on cell lines, the paper's focus shifts to analyzing the epistatic relationship using a different model organism: developing zebrafish larvae.

Through the study, it is noted that rapid cell division as in the case of early stages of zebrafish development, the post-replication methylation is not properly re-established in the daughter cells before the next mitosis commences. In general, the findings suggest that when Dnmt1 enzymatic activity is compromised, there is a reduction in methylation across all three studied sequence contexts (CG dinucleotides, CHG and CHH sites). This observation aligns with the idea that non-CG methylation tends to occur in regions characterized by a high concentration of CG methylation.

To investigate this relationship, the study focused on the genetic aspects and utilized hypomorphic alleles (mutations that cause a partial loss of gene function) of two key genes: dnmt1, responsible for encoding the DNA maintenance methylase Dnmt1, and pole1, responsible for encoding the catalytic subunit of the leading-strand DNA polymerase epsilon holoenzyme (Pole).

In the zebrafish model, homozygous dnmt1 mutants display a genome-wide reduction in DNA methylation levels, whereas the pole1 mutation leads to an increase in DNA methylation levels. Intriguingly, in zebrafish larvae with mutations in both dnmt1 and pole1 (dnmt1/pole1 double mutants), it was observed a restoration of DNA methylation levels to nearly normal values. This restoration is accompanied by a partial rescue of the transcriptional changes and phenotypic traits associated with the individual mutants.

This suggests a balancing antagonism between DNA replication and maintenance methylation, acting as a buffering mechanism against replicative errors. This interplay contributes to the robustness of vertebrate development, emphasizing the intricate relationship between DNA replication, methylation processes, and the overall integrity of genetic information during the critical stages of organismal development.

REFERENCE

Lawir D-F, Soza-Ried C, Iwanami N, Siamishi I, Bylund GO, O´Meara C, et al. Antagonistic interactions safeguard mitotic propagation of genetic and epigenetic information in zebrafish. Communications Biology. 2024;7(1). doi:10.1038/s42003-023-05692-3 

IMAGE CREDITS

The Spruce Pets, https://images.app.goo.gl/fefbNmJthbyXCRbU9

Nature, https://images.app.goo.gl/GLUow8AvBetzXB7F9

ScienceDirect, https://images.app.goo.gl/FaYetvtWZUoZ2uJAA