Chemical approaches for studying histone modifications

Abstract

Histones form the protein core around which genomic DNA is wrapped in eukaryotic chromatin. Numerous genetic studies have established that the structure and transcriptional state of chromatin are closely related to histone post-translational modifications. Further elucidation of the precise mechanistic roles for individual histone modifications requires the ability to isolate and study homogeneously modified histones. However, the highly heterogeneous nature of histone modifications in vivo poses a significant challenge for such studies. Chemical tools that have enabled biochemical and biophysical studies of site-specifically modified histones are the focus of this minireview.

FIGURE 1.

Histones and their PTMs. A, mononucleosome structure with histone tails protruding from the core. This figure was generated from Protein Data Bank code 1KX5 with PyMOL. The colors used for individual histones are the same as described for B. B, schematic representation of histone tails and their modifications. Some modifications at the histone C terminus and globular core are also shown. Groups are indicated as follows: ac, acetyl; Cit, citrullyl; me, methyl; ph, phosphoryl; pr, propionyl; rib, ADP-ribosyl; and Ub, ubiquityl. This figure was adapted from Ref. .

FIGURE 2.

Amber suppression and cysteine-specific modification techniques. A, in vivo amber suppression methodology for incorporating PTMs into histones. 1, (Se)-phenylselenocysteine; 2, N-ϵ-Boc-N-ϵ-methyl-l-lysine; 3, N-ϵ-acetyl-l-lysine. B, conversion of 1 and 2 to modified lysine analogs after incorporation into histones. MeLys, methyllysine; AcLys, acetyllysine. C, in vitro cysteine modification strategy for generating MLAs. Br, bromo.

FIGURE 3.

EPL. Multiple strategies for incorporating synthetic peptides into full-length proteins. SPPS, solid-phase peptide synthesis; RSH, alkyl/aryl thiol.

FIGURE 4.

Semisynthesis of uH2B. A two-step ligation strategy followed by a final desulfurization step yielded native uH2B (5).