DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications

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, 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.

Fig. 1

Chemical modifications of DNA. (a) Cytosine-C5 modifications: enzymes and proteins involved in writing, reading, and erasing the modifications via base-flipping mechanisms. (b) Adenine-N6 methylation: enzymes involved in writing and erasing DNA adenine N6 methylation. (c) Cytosine-N4 methylation

Fig. 2

Writers of DNA modifications. (a) Prokaryotic DNA methyltransferases involved in three different types of DNA methylation have similar structures. DNA is colored in red, and AdoMet/AdoHcy is colored in blue. Flipped bases are shown in green. (b) E. coli AlkB and eukaryotic TET are dioxygenases with common structural folds. αKG is colored in blue, and metal in the active sites is colored in orange

Fig. 3

Readers of DNA modifications. (a) Prokaryotic and eukaryotic SRA domains recognize C5-modified cytosine via base flipping and are similar in structures. (b) Crystal structure of prokaryotic McrB-N monomer flipping 5mC

Fig. 4

Erasers of DNA modifications. (a) Crystal structure of human TDG flipping 5caC opposite guanine. (b) Crystal structure of Geobacillus stearothermophilus endonuclease III in complex with DNA. Iron-sulfur cluster is colored in orange and yellow