Simply Put
Aging is characterized by a loss of DNA compaction in cell nuclei. This leads to dysregulated gene expression and cellular identity. We identified a low abundance modification on histones, which are the proteins around which DNA is wrapped, that seems particularly abundant in human models of exceptional longevity. This modification, i.e. histone succinylation, is a product of cell metabolism of uncertain biological function. We are studying the molecular impact of this modification in “protecting” DNA from anomalous readout by the cell. Our hypothesis is that histone succinylation mitigates the phenomenon of anomalous gene expression occurring during aging. This work will define a new mechanism linking metabolism to gene expression stability and may reveal strategies to maintain genomic integrity and promote healthy aging.
Description
Aging is characterized by progressive loss of chromatin organization, leading to transcriptional dysregulation, genomic instability, and erosion of cellular identity. While epigenetic changes are recognized as central drivers of this process, most work has focused on abundant histone modifications such as methylation and acetylation. In contrast, metabolically derived modifications remain poorly understood, particularly in how they mechanistically influence chromatin structure. Our preliminary data identify histone succinylation as a low-abundance but functionally significant modification enriched in models of exceptional longevity (Stransky et al. Aging Cell, 2026) and capable of modulating key chromatin-regulating enzymes.
In this project, we will investigate histone succinylation as a site-specific regulator of chromatin stability during aging. We hypothesize that succinylation accumulates at defined chromatin domains, where it locally inhibits lysine demethylases (KDM4D and KDM6B), preserves repressive histone methylation marks, and limits aberrant transcription. To test this, we will integrate chromatin profiling, transcriptomic analysis, and biochemical reconstitution in human cell models that recapitulate aging-associated chromatin states.
First, we will define the genomic distribution of histone succinylation relative to repressive chromatin domains. Using long-term, non-replicative 3D human hepatocyte and glial cultures, we will perform quantitative ChIP-seq for succinylation alongside H3K9me3 and H3K27me3. These experiments will determine whether succinylation marks specific regions of preserved heterochromatin or functions at domain boundaries to maintain chromatin insulation. Domain-level analyses will characterize the spatial organization of succinylation and its relationship to chromatin compaction.
Second, we will determine how histone succinylation influences transcriptional output and chromatin structure. By integrating RNA sequencing with chromatin maps, we will assess whether succinylation-enriched domains exhibit reduced transcription, decreased non-coding and antisense RNA production, and lower transcriptional variability. Rather than inducing global repression, we expect succinylation to improve transcriptional fidelity by stabilizing chromatin architecture at specific loci. These analyses will establish a functional link between a metabolically derived histone modification and transcriptional control during aging.
Third, we will establish the direct biochemical mechanism by which histone succinylation inhibits KDM activity. Using recombinant enzymes and site-specifically modified histone substrates, we will perform kinetic and binding assays to determine how succinylation affects enzyme–substrate interactions and catalytic efficiency. These experiments will distinguish substrate-level inhibition from effects of free metabolites and provide definitive evidence for a causal mechanism connecting metabolism, chromatin modification, and gene regulation.
By establishing histone succinylation as a protective regulator of chromatin structure, this project will uncover a previously unrecognized mechanism connecting metabolism to epigenetic stability. These findings may inform strategies to maintain genomic integrity and delay age-associated functional decline.