Methylated & unmethylated arginines as protein docking sites: adding another layer of complexity to the ‘histone code’

PTMs are essential for signal transduction. By altering the biophysical features of proteins, they regulate a diverse array of phenomena including protein subcellular localization, protein stability and protein–protein interactions. When a PTM occurs on histones, it directly modifies chromatin structure and contributes to the organization of higher eukaryotic genomes into euchromatic and heterochromatic domains. Euchromatic domains are important for regulating transcription, by ensuring DNA accessibility, the assembly of the transcription machinery and the binding of sequence-specific transcription factors. Conversely, heterochromatic domains maintain the large majority of the genome in a relatively silent and poorly accessible state. Enzymes such as serine/threonine and tyrosine kinases, lysine acetyltransferases, and lysine and arginine methyltransferases are able to phosphorylate acetylate and methylate histones, respectively. Understanding how these enzymes are regulated is of central importance for understanding how gene transcription and genomic integrity are regulated, and for elucidating the mechanisms controlling key physiological and pathological events such as differentiation, development and cancer. A direct effect of PTMs on chromatin is the alteration of its biophysical and biochemical characteristics and the creation of a dynamic platform upon which the transcriptional machinery is recruited and assembled. The histone code hypothesis suggests that histone PTMs can act as binding sites to be interpreted by chromatin readers and effector proteins. Many nuclear proteins contain motifs such as the bromo domain, that selectively interact with acetylated histones. The ‘Royal family’ domains, which are structurally similar to the prototype chromodomain and bind methyl- ated residues, include the Tudor, Plant–Agenet, PWWP and MBT domains. Recently, other domains have been identified as being able to recognize methylated arginines or lysines. One example is the large family of plant homeodomain (PHD) finger-domains, which are present in several chromatin-associated proteins, and have been demonstrated to interact with methylated lysines and arginines on histone tails. Examples of PHD domain-containing proteins include the tumor suppressor inhibitor of growth 2 (ING2), which binds H3K4me3, and Dnmt3a, which has an ATRX–DNMT3–DNMT3L (ADD) domain containing a PHD finger, and specifically binds to H4R3me2s.

Our lab is interested in how arginine methylation specifically contributes to increase the complexity of the histone code. This is achieved
in two main ways:

1.Methylated arginines can act as docking sites for chromatin-binding proteins on histone tails (Figure 1A);

2.Methylated arginines can act as exclusion marks, impeding the binding of proteins to histones (Figure 1B).