Husna, Amity University Kolkata
What is DNA demethylation?
DNA cytosine methylation is controlled by the functional interplay between two families of enzymes: DNA methyltransferases (DNMTs) and TET methylcytosine dioxygenases, which control DNA methylation and demethylation, respectively. DNA demethylation, as the name suggests, is a process which involves the removal of a methyl group from cytosines. The process can be passive or active.
Enzymes mediating DNA demethylation:
DNA demethylation takes place through oxidation by a family of proteins called ten eleven translocation methylcytosine dioxygenases (TET). TET enzymes help in mediating the process of DNA demethylation by oxidizing 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) respectively. TET enzymes are known to essentially mediate all of the dynamic DNA demethylation activities which occur in mammalian genomes during the embryogenesis, cell lineage specification in developing embryos and organs, and the cell differentiation in response to the various environmental cues.
DNA demethylation can occur through “passive,” replication-dependent dilution when cells divide, since these oxidized methylcytosines (oxi-mCs) are not recognized by the maintenance methyltransferase DNMT1. For a distinct “active” mechanism of DNA demethylation (replication-independent), there should be excision of 5caC and 5fC by the DNA repair enzyme thymine DNA glycosylase (TDG). Additionally, TDG can also excise thymine from mismatched T:G base pairs in DNA efficiently.
Role of enzymes TET and TDG in proliferating and non-proliferating immune cells:
Recently, the role of TET and TDG for DNA demethylation was studied in the proliferating and non-proliferating immune cells.
The respective roles of TET and TDG in T cell and macrophage differentiation was analysed using very deep sequencing to determine DNA methylation status at selected gene loci. To assess the DNA methylation changes during cell differentiation in the absence of DNA replication, bone marrow-derived macrophages stimulated by treatment with liposaccharide (LPS) for 6 h were selected to be examined in mice. These cells undergo cell cycle arrest, do not enter S phase, and stop proliferating in this time frame, but show considerable alterations in the gene expression and activate numerous enhancers as well.
IL-4 gene expression by differentiating Th2 cells was used as the area of focus. It was seen that LPS-treated macrophages accumulate 5hmC at certain enhancers and increase the expression of associated genes without DNA demethylation. Thus, the acute inducible deletion of all three TET genes diminishes Th2 cell differentiation, increases DNA methylation at numerous enhancers and, alters gene expression. Similar acute inducible deletion of TDG, however, had no effect on either DNA demethylation status at the enhancers or Th2 cell differentiation and it didn’t even alter the gene expression in these cells. Moreover, the mice remained healthy even after the acute tamoxifen-mediated deletion of TDG, with essentially normal hematopoiesis for more than 1 year
Overall, it was concluded that demethylation during Th2 differentiation is mainly due to passive DNA demethylation of all three oxidized methylcytosines, with only a very minor contribution (if any) of replication-independent DNA demethylation via TDG. Hence, TET deficiency impairs the Th2 cell differentiation as well as il-4 production but TDG deficiency has little effect.
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Source: Onodera, A., González-Avalos, E., Lio, CW. et al. Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells. Genome Biol 22, 186 (2021). https://doi.org/10.1186/s13059-021-02384-1
Ion Identity Molecular Networking (IIMN)
Hari Krishnan R, SRM Institute of Science and Technology Ion Identity Molecular Networking (IIMN) connects and collapses ion species of the same molecule. Ionization by mass spectrometry causes molecules to form multiple ion species expressing different fragmentation patterns, this causes the formation of redundant and disconnected sub-networks of the same compound species. IIMN is a […]