Base flipping involves rotation of backbone bonds in double-stranded deoxyribonucleic acid (DNA) to expose an out-of-stack base, which can then be a substrate for an enzyme-catalyzed chemical reaction or for a specific protein binding interaction. The phenomenon was first observed for a DNA methyltransferase in 1994 (reference 1), and is now widespread for enzymes or proteins that require access to unpaired, mismatched, damaged or modified bases or even undamaged and unmodified bases for specific functions.
S-adenosyl-l-methionine (AdoMet or SAM) is the second most commonly used enzyme cofactor after ATP. The AdoMet-dependent methyltransferases act on a wide variety of target molecules, including DNA, RNA, proteins, polysaccharides, lipids, and a range of small molecules involved in metabolism. We determined the first structure of a DNA methyltransferase (1993), the first structure of protein arginine methyltransferase (2000), the first structure of a protein (histone) lysine methyltransferase (2002) and its complex with histone peptide substrate (2003). In addition, we determined structures of PvuII, a DNA cytosine-N4 methyltransferase (1997), DNMT2 - a tRNA cytosine methyltransferase (2001), HNMT - a small molecule (histamine) methyltrasnferase (2001), HemK - a protein glutamine methyltransferase (2004), Dot1p - a histone H3 lysine79 methyltransferase (2004), and SETD6 - a non-histone lysine methyltransferase (2011).
5. Dong A, Yoder JA, Zhou L, Zhang X, Bestor T, Cheng X (2001) Structure of human DNMT2, an enigmatic DNA methyltransferase homologue that displays denaturant-resistant binding to DNA. Nucleic Acids Res. 29, 439-448.
6. Horton JR, Sawada K, Nishibori M, Zhang X, Cheng X (2001) Two polymorphic forms of human histamine methyltransferase: structural, thermal and kinetic comparisons. Structure, 837-849.
In addition to cytosine C5 modification (5mC) in DNA and RNA, the exocyclic amino group of adenine in DNA and RNA is also methylated, resulting in N6-methyl-adenine (N6mA).
Chromatin regulates transcriptional processes through postsynthetic modifications of both of its components: DNA and histones. Much remains to be learned about how the combination of these modifications (or lack thereof) facilitates or silences transcription. One broad theme has emerged that a web of interactions tightly coordinates the modification of a segment of DNA and its associated histones, affecting local chromatin structure and determining the functional states. We are the first to illustrate the mechanistic insights of anti-correlation of histone H3 lysine 4 (H3K4) methylaion and DNA methylation (2007), coordinated methylations of H3K9 and DNA (2011), and a methyl-and-phospho switch in DNMT1 (2011).
In principle, epigenetic modifications alter the interaction with DNA binding proteins by strengthening, weakening, or abolishing the interaction altogether. This, in turn, can modulate gene expression and control cellular metabolism and is believed to be one of the principal mechanisms underlying epigenetic processes such as differentiation, development, aging, and disease. We have identified and determined structures of reader domains recognizing histone and DNA modifications (or lack thereof).
We illustrated the mechanistic insight of anti-correlation of H3K4 and H3K9 methylation by PHF8 (2010). The crosstalk between different modifications also applies to non-histone proteins such as ERα (2008) and NF-κB (2011).
Histone lysine methylation is often compromised in cancers, and the corresponding enzymes (methyltransferases and demethylases) have since become important therapeutic targets, particularly in human cancers where these enzymes are frequently mutated and/or misregulated.
The Krüppel-associated box (KRAB) domain containing Cys2–His2 (C2H2) zinc finger (ZF) proteins are the largest family of transcription factors/regulators in vertebrates that expanded and diversified during vertebrate evolution.
A Watson-Crick base pair of Guanine (left) and 5-carboxylcytosine (right).