Histone methylation regulates gene expression
In eukaryotic cells, the genome is assembled into chromatin which, on the one hand, solves the basic packaging problem and, on the other, provides a dynamic platform for controlling all DNA-mediated processes within the nucleus.
The basic unit of chromatin is the nucleosome core particle – it contains a 147-base pair DNA wrapped almost twice around an octamer of the core histone proteins. The octamer comprises a central heterotetramer of histones H3 and H4, flanked by two heterodimers of histones H2A and H2B.
Lysine methylation
Histone lysine (K) methylation has been found to be a crucial player in gene regulation. One of the best-studied methylation marks is at the 79th position of histone H3 protein (H3K79). The residue is located in the solvent-exposed region of H3. Like multiple lysine residues, H3K79 is subject to postsynthetic methylation by a host of methyltransferases (writers) – the methyl mark can also be removed by histone lysine demethylases (erasers).
Interestingly, unlike acetylation and phosphorylation, which can not only recruit various proteins to chromatin but also directly affect chromatin structure by altering the charge of the histones, methylation of lysine does not alter the effective charge, but the hydrophobic and steric properties. Methylated lysine modulates chromatin structure through the recruitment of “reader” proteins that facilitate transcriptional activation or repression.
Menin – an H3K79me2 reader
Human Menin, a tumor repressor protein, has been identified as a “bona fide reader” of H3K79me2 (Lin et al. SCIENCE 17 February 2023). It is a scaffold protein that can interact with a multitude of proteins with diverse cellular functions, and both positively as well as negatively regulate gene expression.
Human Menin is a 610 amino acid residue long polypeptide. It consists of an N-terminal domain, a thumb domain, a helical palm domain and a C-terminal fingers domain. All four domains are said to be important for the in vivo function of Menin.
A recent paper (Menin “reads” H3K79me2 mark in a nucleosomal context) by Lin et al. in SCIENCE (17 February 2023) has shown that Menin engages with the nucleosome using its palm and fingers domains and “reads” the methylation mark through a p-cation interaction.
Electrostatics in action
Paradoxically, it was found that water-soluble cationic molecules prefer a hydrophobic cavity to the aqueous medium, if the cavity was lined with p-systems. What underlies this phenomenon is the cation-p interaction. In a variety of proteins, including neuroreceptors and ion channels, a general structural motif for cation-p interaction is the so called “aromatic box” (Davis, M. R. and Dougherty, D. A. Phys Chem Chem Phys, 2015, 17, 29262). An aromatic box, consisting of three tyrosine (Tyr) and two tryptophan (Trp) residues, was revealed in the acetylcholine binding protein (AChBP). This box binds the cationic moiety of acetylcholine (ACh).
While van der Waals and polarization effects do contribute to the cation-pi interaction, but the interaction is predominantly electrostatic. In aromatic amino acids, such as tryptophan and tyrosine, there are six (four) local C d- – H d+ bond dipoles around the aromatic ring. Quantum mechanical calculations show that there is a build-up of negative electrostatic potential on the face of the p system. This is the region to which cations bind
The cation-pi interaction is one of the strongest driving forces in the formation of biomolecular complexes. Lysine or arginine side chains (positively charged) of a large number of proteins interact with phenylalanine, tyrosine or tryptophan through pi-cation interactions. The figure below illustrates how the cationic H3K79me2 can possibly be (electrostatically) “read” by a putative aromatic box.