Nuclear Acetyl-CoA Compartment-Switching as a Bidirectional Epigenetic Thermostat of Organismal Aging

Nuclear acetyl-CoA pools act as a bidirectional epigenetic thermostat governing organismal aging. ACLY-mediated acetyl-CoA generation drives pathological hypoacetylation at silent gene promoters, while ACSS2-mediated pools maintain protective hyperacetylation at active longevity gene loci. The ratio of nuclear ACLY:ACSS2 activity determines whether aging manifests as transcriptional silencing (senescence) or chromatin loosening (expression errors).

Aged MSCs show reduced nuclear acetyl-CoA from impaired mitochondrial citrate export via CiC, which silences osteogenic genes [1]. Middle-aged flies, by contrast, display histone overacetylation that increases expression errors [2]. These apparently contradictory findings likely reflect distinct enzymatic sources: the first stems from ACLY deficiency—citrate-derived acetyl-CoA that normally supports repressed genes—while the second may represent ACSS2 dysregulation, affecting acetate-derived acetyl-CoA at active loci. Calorie restriction illustrates this nicely: it decreases ACLY-derived cytoplasmic pools while increasing ACSS2-derived nuclear pools for longevity gene activation [3].

This mechanism proposes that ACLY and ACSS2 generate nuclear acetyl-CoA pools with non-overlapping genomic targeting. ACLY preferentially supplies acetyl-CoA to silenced gene promoters via p300/CBP, maintaining repressive histone marks that become deficient with age. ACSS2, meanwhile, supplies active enhancers and autophagy genes including TFEB targets [4]. Mitochondrial dysfunction during aging selectively impairs ACLY pathway flux without affecting nuclear ACSS2 translocation, creating locus-specific hypoacetylation. However, chronic acetate supplementation or ACSS2 overexpression can overshoot, generating excessive acetyl-CoA at active loci—explaining the fly overacetylation phenotype.

This hypothesis yields several testable predictions: (1) ChIP-seq of H3K27ac in aged human tissues will show decreased marks at ACLY-target promoters but increased marks at ACSS2-target enhancers; (2) Dual modulation—increasing ACLY while limiting ACSS2—will synergistically restore proper acetylation balance; (3) The hypothalamic nuclear acetyl-CoA pool, critical for organismal aging [5], will show opposite ACLY:ACSS2 ratios compared to mesenchymal stem cells, explaining tissue-specific aging phenotypes.

This framework resolves the paradox of hypo- versus hyperacetylation in aging by proposing that the therapeutic window requires selective enzyme modulation rather than global histone acetylation manipulation.

[1] https://www.genengnews.com/news/epigenetic-changes-in-aging-stem-cells-rejuvenated-by-acetate/ [2] https://www.gowinglife.com/overactive-protein-acetylation-connected-to-the-aging-process/ [3] https://pubmed.ncbi.nlm.nih.gov/33917812/ [4] https://pubmed.ncbi.nlm.nih.gov/33917812/ [5] https://pubmed.ncbi.nlm.nih.gov/33917812/