Effect of exogenous histone H5 on integration of histone H1 in rat liver chromatin. Correlations with aberrant epsilon-N-methylation of histone H1

Quantitative analysis of histone modifications: formaldehyde is a source of pathological n(6)-formyllysine that is refractory to histone deacetylases

Aberrant protein modifications play an important role in the pathophysiology of many human diseases, in terms of both dysfunction of physiological modifications and the formation of pathological modifications by reaction of proteins with endogenous electrophiles. Recent studies have identified a chemical homolog of lysine acetylation, N⁶-formyllysine, as an abundant modification of histone and chromatin proteins, one possible source of which is the reaction of lysine with 3′-formylphosphate residues from DNA oxidation. Using a new liquid chromatography-coupled to tandem mass spectrometry method to quantify all N⁶-methyl-, -acetyl- and -formyl-lysine modifications, we now report that endogenous formaldehyde is a major source of N⁶-formyllysine and that this adduct is widespread among cellular proteins in all compartments. N⁶-formyllysine was evenly distributed among different classes of histone proteins from human TK6 cells at 1–4 modifications per 10⁴ lysines, which contrasted strongly with lysine acetylation and mono-, di-, and tri-methylation levels of 1.5-380, 5-870, 0-1400, and 0-390 per 10⁴ lysines, respectively. While isotope labeling studies revealed that lysine demethylation is not a source of N⁶-formyllysine in histones, formaldehyde exposure was observed to cause a dose-dependent increase in N⁶-formyllysine, with use of [¹³C,²H₂]-formaldehyde revealing unchanged levels of adducts derived from endogenous sources. Inhibitors of class I and class II histone deacetylases did not affect the levels of N⁶-formyllysine in TK6 cells, and the class III histone deacetylase, SIRT1, had minimal activity (<10%) with a peptide substrate containing the formyl adduct. These data suggest that N⁶-formyllysine is refractory to removal by histone deacetylases, which supports the idea that this abundant protein modification could interfere with normal regulation of gene expression if it arises at conserved sites of physiological protein secondary modification.

Oxidative stress and inflammation lead to the generation of a multitude of electrophiles in cells that in turn react with nucleophilic macromolecules such as DNA, RNA, polyunsaturated fatty acids, and proteins, leading to progression of a variety of disorders and diseases. Emerging evidence points to widespread modification of cellular proteins by N⁶-formylation of lysine as a result of adventitious reactions with endogenous electrophiles. N⁶-Formyllysine is a chemical homolog of the biologically important N⁶-acetyllysine and thus may interfere with acetylation signaling in cells. While N⁶-formyllysine adducts are now well recognized as abundant protein modifications in cells, the source of these pathological adducts remains unclear. Our previous study proposed N⁶-formylation of lysine in histone proteins occurred by reaction of lysine with 3′-formylphosphate residues arising from DNA oxidation. Here, we investigate additional sources as well as the fate of this abundant pathological protein modification. Our results reveal that endogenous formaldehyde is a major source of N⁶-formyllysine and that this adduct is widely distributed among proteins in all cell compartments. We also demonstrate for the first time that N⁶-formyllysine modifications do not undergo appreciable removal by histone deacetylases, which suggests that they persist in proteins and possibly interfere with the signaling functions at conserved lysine positions in histone proteins.

Use of double spin-labeled histones to monitor histone-chromatin integration

Tyrosine-specific nitroxide spin labels have been synthesized that utilize either deuterium or deuterium and [15N] isotopic substitution within the nitroxide ring. These probes have been used to differentially spin label and simultaneously monitor both histones H1 and H5, during the displacement of endogenous spin-labeled H1 from reconstituted chromatin by exogenously added spin-labeled H5.