Hibernating Hamsters Rewrite Their Histones, Not Their DNA, to Survive Winter

Every winter, the Syrian hamster performs one of biology’s most remarkable feats: it switches its body into a state of profound torpor, dropping its metabolism and core temperature to levels that would be lethal to most mammals, and then reverses the process hours or days later with no apparent harm. How a warm-blooded animal can dial its own physiology down and back up again, on demand, has fascinated scientists for decades. A new study published in Epigenetics Communications offers a detailed molecular clue, showing that the answer may lie not in the animal’s DNA sequence, nor even in the chemical tagging of that DNA, but in the dynamic decoration of the proteins around which the genome is wound.

The research, led by Marloes Oosterhof and Louis Coussement of the University of Groningen together with colleagues in Belgium, Austria and the Netherlands, focused on the liver, the metabolic command center that manages the fuel switch from glucose to fat oxidation that hibernation demands. Because facultative hibernators like the Syrian hamster enter torpor only in response to environmental cues, shortening days, cold and food scarcity, their bodies must actively reprogram gene expression rather than simply follow a fixed seasonal clock. That flexibility makes epigenetic mechanisms, the chemical systems that switch genes on and off without altering the underlying sequence, prime suspects for orchestrating the transition.

To test this idea, the team induced hibernation in Syrian hamsters by shortening the light-dark cycle and lowering ambient temperature, then collected liver samples at carefully defined phases: summer euthermia, when animals were active and warm; late torpor, more than 72 hours after the animals had settled into a bout; and both early and late arousal, shortly after the animals rewarmed. Using infrared motion detectors, the researchers confirmed each animal’s state before euthanasia, ensuring that the molecular snapshots truly reflected the hibernation phase rather than guesswork about body temperature.

The first layer of analysis examined the expression of 94 genes encoding epigenetic writer and eraser enzymes, the proteins that add or remove chemical marks on histones and DNA. Of the 83 genes that could be reliably measured, 11 shifted significantly between phases. Strikingly, four histone acetyltransferases, KAT6A, KAT6B, KAT7 and KAT13D, better known as the circadian gene CLOCK, were differentially expressed, with most declining during torpor and rebounding during arousal. Three deacetylases, SIRT2, SIRT7 and HDAC11, also changed, along with two histone methyltransferases, one demethylase and the DNA demethylating enzyme TET2.

Notably, several of these enzymes, including PCAF, GCN5L2, HAT1 and CBP, had been flagged in previous work on the thirteen-lined ground squirrel, an obligatory hibernator, but showed no expression changes in the hamster. This divergence suggests that facultative hibernators may deploy a distinct epigenetic toolkit, one tailored to switching hibernation on and off in response to the environment rather than to an internal circannual rhythm. The downregulation of CLOCK in the hamster liver is particularly intriguing, since recent work indicates that the liver pauses its circadian rhythms during hibernation while the brain retains them.

Gene expression, however, is only an indirect readout. The team therefore measured histone acetylation directly, first by Western blot and then by quantitative mass spectrometry, a technique that can determine exactly how many acetyl groups sit on specific lysine residues of histones H3 and H4. The results were consistent and telling. Overall acetylation of histone H3 dropped during late torpor, with the acetylation of lysines 18 and 23 falling by roughly 5 and 14 percent respectively, and rising again during arousal. H3K27ac, a mark classically associated with active enhancers and open chromatin, was lowest in torpor and recovered as animals rewarmed, a pattern that fits the idea of chromatin condensing, and transcription shutting down, while the animal is cold and metabolically dormant.

Histone H4 told a subtler story. Unlike H3, whose acetylation largely rebounded during arousal, the H4 peptide spanning lysines 5, 8, 12 and 16 remained under-acetylated even after the animals had rewarmed. The single most heavily used site, H4K16, a modification with the unusual ability to both promote and repress transcription depending on context, was significantly less acetylated in late arousal than in summer-active animals. The researchers point to SIRT2 and SIRT7, both of which target H4K16 and both of which were upregulated during arousal, as plausible culprits, noting that these sirtuins can translocate into the nucleus during cell-cycle transitions and stress, both of which accompany the metabolic turbulence of rewarming.

On the enzyme-activity side, histone acetyltransferase activity stayed flat across all phases, but histone deacetylase activity peaked in late torpor. Inhibitor profiling revealed that a single enzyme, HDAC6, accounted for roughly 71 percent of total hepatic HDAC activity. Yet here the plot thickened: although HDAC6 activity was high and histone acetylation low during torpor, the acetylation of alpha-tubulin, HDAC6’s best-known cytosolic target, actually increased. The authors suggest that HDAC6 may relocate to the nucleus during torpor, deacetylating histones there while leaving tubulin untouched, and note that the enzyme is also tied to hepatic gluconeogenesis and to protective responses in ischemic liver injury, processes highly relevant to both hibernation and, potentially, human organ preservation.

Perhaps the most surprising negative result concerned DNA methylation. Using both the Luminometric Methylation Assay and whole-genome bisulfite sequencing, the team found no significant differences in global cytosine methylation at CpG or non-CpG sites across any hibernation phase, and promoter methylation of the differentially expressed genes was likewise unchanged. This stability mirrored the near-absence of changes in the expression of DNA methyltransferases and demethylating enzymes, and it contrasts with reports of methylation shifts in ground squirrels and horseshoe bats. In the Syrian hamster, at least, the epigenetic levers of hibernation appear to be pulled at the histone level rather than at the DNA level.

The broader implications reach well beyond rodent physiology. Because facultative hibernators can trigger hypometabolic, cytoprotective states essentially on command, understanding their epigenetic switches could inform strategies to protect organs during transplantation, to limit ischemic damage, and even to slow aging, given recent evidence that epigenetic aging is effectively stalled during hibernation in yellow-bellied marmots. The authors caution that their bulk liver measurements largely reflect hepatocytes and that single-cell follow-up work will be needed to resolve contributions from rarer cell types, and that the expression changes, though modest in fold change, match the magnitude of the measured histone modifications. Still, the message is clear: when a hamster decides to hibernate, it does not rewrite its DNA. It retunes the packaging, loosening and tightening the spools of chromatin to silence the genome through the cold and swing it back open for the warmth of arousal.

Subject of Research: Epigenetic regulation of gene expression, specifically histone acetylation and DNA methylation, in the liver of facultatively hibernating Syrian hamsters

Article Title: Changes in histone lysine acetylation, but not DNA methylation during facultative hibernation in Syrian hamster liver

Article References: Oosterhof, M. M., Coussement, L., van Pijkeren, A., Kwiatkowski, M., Zwinderman, M. R. H., Dekker, F. J., de Meyer, T., Reitsema, V. A., Bischoff, R., Guryev, V., Bouma, H. R., Henning, R. H., & Rots, M. G. (2024). Changes in histone lysine acetylation, but not DNA methylation during facultative hibernation in Syrian hamster liver. Epigenetics Communications, 4(1), Article 1. https://doi.org/10.1186/s43682-023-00024-2

Image Credits: AI Generated

DOI: 10.1186/s43682-023-00024-2

Keywords: hibernation, Syrian hamster, epigenetics, histone acetylation, DNA methylation, HDAC6, sirtuins, liver metabolism, torpor, chromatin, KAT6A, epigenetics communications