The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine

Abstract

DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our understanding of cellular programming and responses to environmental cues. One of the key modifications, m⁵C, has been identified as a contributor to regulation of the DNA damage response (DDR). However, the various mechanisms of dynamic m⁵C deposition and removal, and the role m⁵C plays within the cell, remains to be fully understood.

Keywords: DNA; DNA damage; RNA; cancer; demethylases; hm5C; m5C; methyltransferases.

FIGURE 1

DNA methylation and demethylation machinery. DNA methyltransferase 3A (DNMT3A) and DNA methyltransferase 3B (DNMT3B) are responsible for the creation of DNA methylation patterns. DNA methyltransferase 3L (DNMT3L) interacts and stimulates DNMT3A and DNMT3B methylation activity. DNA methyltransferase 1 (DNMT1) is actively involved in the maintenance of DNA methylation patterns. Passive demethylation occurs in the absence of functional DNMT1, which methylates DNA after each cellular division. Active demethylation is mediated by Ten-eleven Translocation (TET) dioxygenases. TET enzymes oxidize 5-methylcytosine (m⁵C) to produce 5-hydroxymethylcytosine (hm⁵C), 5-formylcytosine (f⁵C) and 5-carboxylcytosine (ca⁵C). The glycosylase activity of TDG allows the excision of Tet-produced f⁵C or ca⁵C nucleobases. Created with BioRender.com.

FIGURE 2

Distribution of m⁵C and hm⁵C post-transcriptional modifications on mRNA molecules. 5-methylcytosine (m⁵C) is predominantly found in 5′ untranslated regions (5′ UTRs), while 5-hydroxymethylcytosine (hm⁵C) is present within the coding sequence (CDS). Created with BioRender.com.