Faculty, Staff and Student Publications
Publication Date
1-1-2022
Journal
Advances in Experimental Medicine and Biology
Abstract
The modification of DNA bases is a classic hallmark of epigenetics. Four forms of modified cytosine-5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine-have been discovered in eukaryotic DNA. In addition to cytosine carbon-5 modifications, cytosine and adenine methylated in the exocyclic amine-N4-methylcytosine and N6-methyladenine-are other modified DNA bases discovered even earlier. Each modified base can be considered a distinct epigenetic signal with broader biological implications beyond simple chemical changes. Since 1994, several crystal structures of proteins and enzymes involved in writing, reading, and erasing modified bases have become available. Here, we present a structural synopsis of writers, readers, and erasers of the modified bases from prokaryotes and eukaryotes. Despite significant differences in structures and functions, they are remarkably similar regarding their engagement in flipping a target base/nucleotide within DNA for specific recognitions and/or reactions. We thus highlight base flipping as a common structural framework broadly applied by distinct classes of proteins and enzymes across phyla for epigenetic regulations of DNA.
Keywords
5-Methylcytosine, Cytosine, DNA, DNA Methylation, Epigenesis, Genetic, Eukaryota, Epigenetic methylation; DNA base flipping; Reader, writer and eraser of DNA methyl marks; Methyltransferases; Demethylases
DOI
10.1007/978-3-031-11454-0_12
PMID
36350515
PMCID
PMC9711002
PubMedCentral® Posted Date
11-30-2022
PubMedCentral® Full Text Version
Author MSS
Published Open-Access
yes
Included in
Bioinformatics Commons, Biomedical Informatics Commons, Genetic Phenomena Commons, Medical Genetics Commons, Oncology Commons