Protein hyperacylation links mitochondrial dysfunction with nuclear organization

Abstract

Cellular metabolism is linked to epigenetics, but the biophysical effects of metabolism on chromatin structure and implications for gene regulation remain largely unknown. Here, using a broken tricarboxylic acid (TCA) cycle and disrupted electron transport chain (ETC) exemplified by succinate dehydrogenase subunit C (SDHC) deficiency, we investigated the effects of metabolism on chromatin architecture over multiple distance scales [nucleosomes (~10^2 bp), topologically-associated domains (TADs; ~10^5 - 10^6 bp), and chromatin compartments (10^6 - 10^8 bp)]. Metabolically-driven hyperacylation of histones led to weakened nucleosome positioning in multiple types of chromatin, and we further demonstrate that lysine acylation directly destabilizes histone octamer-DNA interactions. Hyperacylation of cohesin subunits correlated with decreased mobility on interphase chromatin and increased TAD boundary strength, suggesting that cohesin is metabolically regulated. Erosion of chromatin compartment distinctions reveals metabolic regulation of chromatin liquid-liquid phase separation. The TCA cycle and ETC thus modulate chromatin structure over multiple distance scales.

Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism

“…In addition to site‐specific acylations, global Kac, Kpr, Kbu, Kmal, and Ksucc of histones can weaken nucleosome stability, histone‐DNA interactions and promote nucleosome sliding. Of these modifications, Ksucc has the longest acyl‐CoA chain and imparts a negative charge, which might explain why it was able to destabilize nucleosomes to the greatest extent in an optical tweezer approach using 12‐mer nucleosomal arrays (preprint: Smestad et al , 2020). In general, single‐molecule force spectroscopy techniques, such as optical or magnetic tweezers, can be used to study the stability of clamped mononucleosomes and nucleosomal arrays by applying an accurate force and measuring motions (Fig 2C) (Neuman & Nagy, 2008).…”

Roles of Negatively Charged Histone Lysine Acylations in Regulating Nucleosome Structure and Dynamics

“…A cellular function study of Sirt7 revealed that the Sirt7-catalyzed desuccinylation of H3K122 promoted chromatin condensation and DNA-damage repair ( Li et al, 2016 ). Moreover, metabolically driven hypersuccinylation of histones was reported to weaken nucleosome stability ( Smestad et al, 2020 ), further underlining the general effects of lysine succinylation on nucleosome dynamics.…”