Characterizing the movement, interactions, and chemical microenvironment of a protein inside the living cell is crucial to a detailed understanding of its function. Most strategies aimed at realizing this objective are based on genetically fusing the protein of interest to a reporter protein that monitors changes in the environment of the coupled protein. Examples include fusions with fluorescent proteins, the yeast two-hybrid system, and split ubiquitin. However, these techniques have various limitations, and considerable effort is being devoted to specific labeling of proteins in vivo with small synthetic molecules capable of probing and modulating their function. These approaches are currently based on the noncovalent binding of a small molecule to a protein, the formation of stable complexes between biarsenical compounds and peptides containing cysteines, or the use of biotin acceptor domains. Here we describe a general method for the covalent labeling of fusion proteins in vivo that complements existing methods for noncovalent labeling of proteins and that may open up new ways of studying proteins in living cells.

We report here the generation of mutants of the human O(6)-alkylguanine-DNA alkyltransferase (hAGT) for the efficient in vivo labeling of fusion proteins with synthetic reporter molecules. Libraries of hAGT were displayed on phage, and mutants capable of efficiently reacting with the inhibitor O(6)-benzylguanine were selected based on their ability to irreversibly transfer the benzyl group to a reactive cysteine residue. Using synthetic O(6)-benzylguanine derivatives, the selected mutant proteins allow for a highly efficient covalent labeling of hAGT fusion proteins in vivo and in vitro with small molecules and therefore should become important tools for studying protein function in living cells. In addition to various applications in proteomics, the selected mutants also yield insight into the interaction of the DNA repair protein hAGT with its inhibitor O(6)-benzylguanine.

Histones are subject to a wide variety of post-translational modifications that play a central role in gene activation and silencing. We have used histone modification-specific antibodies to demonstrate that two histone modifications involved in gene activation, histone H3 acetylation and H3 lysine 4 methylation, are functionally linked. This interaction, in which the extent of histone H3 acetylation determines both the abundance and the "degree" of H3K4 methylation, plays a major role in the epigenetic response to histone deacetylase inhibitors. A combination of in vivo knockdown experiments and in vitro methyltransferase assays shows that the abundance of H3K4 methylation is regulated by the activities of two opposing enzyme activities, the methyltransferase MLL4, which is stimulated by acetylated substrates, and a novel and as yet unidentified H3K4me3 demethylase.A growing body of evidence suggests that many different types of post-translational histone modifications play key roles in regulating gene expression and that some modifications at least are functionally inter-related (1). The linked deposition of distinct modifications can occur both on the same histone tail, e.g. H3S10 phosphorylation and H3K9 acetylation (2) or on different tails, e.g. H2A ubiquitination and H3 methylation (3), histone acetylation, and methylation (4, 5). Multiprotein complexes have been identified that are capable of depositing, or removing, different modifications in a coordinated manner (e.g. histone demethylase and deacetylase activity in coREST) (6). Similarly, binding proteins are sensitive to combinations of modifications; for example, HP1 binding to the H3 tail requires histone H3K9 methylation but is blocked by H3S10 phosphorylation and H3K14 acetylation (Ref. 7, although see Ref. 8).This suggests that epigenetic marks are not deposited or recognized in isolation but comprise a complex and inter-related collection of modifications at adjacent residues.The correlation between different histone modifications is particularly clear for histone H3 acetylation and the methylation of histone H3 lysine 4 (H3K4me). Mass spectrometric analysis of the cellular pool of histones indicates that this methyl mark is associated with histone H3 molecules containing high levels of acetylation (9). This is consistent with the observed co-localization of these marks, which show related distribution patterns both at a chromosome-wide level during X inactivation (10) and over the coding regions of individual genes (11,12). These correlations may arise due to physical links between histone-modifying enzymes such that they are co-recruited to the same loci. Both MLL1, a histone methyltransferase (HMT) 2 that can generate H3K4me marks (13), and Chd1, the chromatin remodeler that is subsequently recruited by this methyl mark, associate with histone acetyltransferase activities (14, 15), whereas the LSD1 complex that removes some of these methyl marks contains the histone deacetylases HDAC1 and HDAC2 (16). However, the interaction could also arise ...

No abstract

We present here a novel approach to induce protein dimerization in living cells through covalent labeling of fusion proteins with ligands which are interacting with other proteins. The covalent labeling is based on the reaction of the DNA repair protein O6-alkylguanine-DNA alkyltransferase with O6-benzylguanine coupled to an appropriate ligand. Using methotrexate as a ligand, it is shown that the approach can be used to control transcription in the yeast Saccharomyces cerevisiae. The specificity of the labeling reaction and its irreversible nature should allow the approach to become a valuable tool to study and control protein dimerization in vivo.