Reversible histone glycation is associated with disease-related changes in chromatin architecture

Qingfei Zheng,Shixin Liu,Yael David,Hannah D’Ambrosio,Adewola Osunsade,Albert S Agustinus,Nathaniel D Omans,Sarat Chandarlapaty,Bo Liu,Efrat Finkin-Groner,Rachel Leicher

doi:10.1038/s41467-019-09192-z

Abstract

Cellular proteins continuously undergo non-enzymatic covalent modifications (NECMs) that accumulate under normal physiological conditions and are stimulated by changes in the cellular microenvironment. Glycation, the hallmark of diabetes, is a prevalent NECM associated with an array of pathologies. Histone proteins are particularly susceptible to NECMs due to their long half-lives and nucleophilic disordered tails that undergo extensive regulatory modifications; however, histone NECMs remain poorly understood. Here we perform a detailed analysis of histone glycation in vitro and in vivo and find it has global ramifications on histone enzymatic PTMs, the assembly and stability of nucleosomes, and chromatin architecture. Importantly, we identify a physiologic regulation mechanism, the enzyme DJ-1, which functions as a potent histone deglycase. Finally, we detect intense histone glycation and DJ-1 overexpression in breast cancer tumors. Collectively, our results suggest an additional mechanism for cellular metabolic damage through epigenetic perturbation, with implications in pathogenesis.

Highlights

Cellular proteins continuously undergo non-enzymatic covalent modifications (NECMs) that accumulate under normal physiological conditions and are stimulated by changes in the cellular microenvironment
Oxidative stress due to increase in reactive oxygen species (ROS) enhances the formation of advanced glycation end-products (AGEs), which in turn increases the presence of ROS in a positive feedback loop termed glycoxidation[5]
It is noteworthy that glycation on H3 compromises the anti-H3 epitope, causing a decrease in the overall anti-H3 signal in response to treatment with increased MGO concentration (Supplementary Figure 1, Supplementary Table 3)

Summary

Results

H3 is the prime target for MGO glycation. MGO is an important glycolysis by-product, which was shown to modify proteins as well as DNA and has been implicated in contributing to cancer cell formation and metastasis[10,18]. It is noteworthy that glycation on H3 compromises the anti-H3 epitope, causing a decrease in the overall anti-H3 signal in response to treatment with increased MGO concentration (Supplementary Figure 1, Supplementary Table 3) To examine this selective reactivity in a more physiologically relevant context, we turned to reconstituted NCPs. Composed of recombinant wild-type histones and a minimal 147 bp ‘601’ DNA fragment[19], NCPs represent the fundamental unit of chromatin. Reconstituted NCPs were incubated with higher ratios of MGO for 72 h, after which they were separated by SDSPAGE and analyzed by western blot with anti-MGO This analysis revealed glycation adducts and rearranged cross-linked products forming in a concentration-dependent manner, where similar to the purified histones, H3 is the primary site of glycation (Fig. 2b, Supplementary Table 3).

Anti-H3K9me3 Anti-H3K4me3

Anti-H3

Methods