How what we eat influences epigenetics: a study on methionine restriction

da | Giu 4, 2021 | Biologia Molecolare

Abstract

Chromatin methylation has been shown to be particularly susceptible to diet-related stresses. SAM depletion induced by methionine restriction elicits a metabolic response that is involved in the maintenance of the epigenetic pattern. The residue H3K9 was found to be crucial in this response, indeed Haws and collaborators (1) have found an increase of H3K9me1 in regions previously marked by both H3K9me2/3 or unmethylated H3K9. The maintenance of the monomethylation on H3K9 was found to be essential for the epigenetic persistence. This discovery could inspire further research in this field.

In the last few years there has been a growing interest in the interplay between epigenetics and metabolism, as both animals and humans often go through several diet-related stresses throughout their lives. In particular, few metabolites such as NAD+, Acetyl-CoA and SAM were found to be critical for epigenetic modifications, as they are cofactors of histone modification enzymes (2).

Low methionine diet was found to be correlated to lifespan extension in mammals (3) as it has been found to be associated with an increase in cardioprotective hormones, a decrease in ROS levels, a reduction in triglycerides and rescue from severe steatosis (4). Conversely, it has been demonstrated that a complete restriction of methionine (Met) is involved in an aggravation of chronic liver diseases (5).

Recently, Haws et al.  investigated the role of S-adenosyl methionine (SAM), that is the major donor of histone methylases and is involved in methionine cycle. To assess the contribution of SAM depletion in both histone post-translational modifications and DNA methylation, the researchers employed both in vitro (HCT116 cell) and in vivo (mouse) models kept under methionine restriction. By mass spectrometry analysis (LC-MS/MS), they found that, even if levels of Met and SAM were reduced, DNA methylation was not affected, histone di- and tri-methylation was reduced concomitantly to an increase of acetylated or non-modified histones.

Subsequently, in order to evaluate if Met-restricted diet was a good model to mimic SAM depletion, two different approaches were used: 1) RNAi knockdown of MAT2A (SAM synthetase gene) and 2) overexpression of PEMT, the major consumer of SAM. Data showed that the two methods are comparable to Met restriction both in vivo and in vitro models.  They found a global increase H3K9ac and H3K9un, a decrease in H3K9me2/3, while H3K9me1 was maintained and stable. This analysis revealed a conserved response of H3K9 PTMs, suggesting that Lysin 9 of the Histone H3 may be the main player in the organism response following the lack of SAM.

EHMT1/2 were found to be the main H3K9 methyltransferases in their system. To study the role of H3K9 methylation in SAM depletion, the researchers used the UNC0642 (EHMT1/2 inhibitor) in order to block de novo H3K9 methylation. A LC-MS/MS analysis revealed that coupling Met restriction with UNC0642 caused a significant decrease of H3K9me1, while H3K9me2 levels remained similar to Met restriction without the treatment with UNC0642. Therefore, during SAM depletion EHMT1/2 have a preferential activity toward the creation of H3K9me1.

To determine the contribution of cytoplasmatic and nuclear H3K9me1 during Met restriction, a SILAC experiment was performed and revealed that ~40% of mono methylation is added half in the cytoplasm and half in the nucleus and the remaining ~60% derives from H3K9me1 turnover protection or via H3K9me2/3 demethylation.

By observing ChIP-seq results it was clear that during SAM depletion there was a global change in histone PTMs: H3K9me3 was substituted by H3K9me1 in constitutively repressed regions such as repetitive and transposable genomic loci. H3K9me1 was already known to serve as a primer for higher state methylation, however Hawks et al. demonstrated that during SAM depletion this PTM also preserves heterochromatin stability. Indeed, qRT-PCR revealed that the transcription of constitutively repressed LINE1 and HERV-K was found to be strongly upregulated comparing treatment with UNC0642 to the control.

Furthermore, using MNase accessibility assay, it was also observed that the repression of mono methylation by EHMT1/2 was correlated with an increase in euchromatin. After repleting the media with methionine, mock treated (DMSO) cells were similar to the untreated, since they returned to their pre-Met restriction state. Conversely, both histone PTMs and transcripts of cells treated with methylase inhibitor UNC0642 were found to be still dysregulated. Indeed, they were significantly diverse compared to the untreated and, more importantly, to the Met-repleted control cells. All together, these data lead to the hypothesis that H3K9me1 is the key player for epigenetic persistence.

By administering 3 weeks of Met restriction followed by 5 weeks of Met repletion to mice, the researchers were also able to observe that in vivo recovery from SAM depletion is conserved and similar in 6- and 22-months old mice as they were back to their original state without age-related differences.

Figure 2 – General scheme (Created with BioRender.com)

In conclusion, Haws et al. discovered that mono methylation of H3K9 is an adaptive epigenetic response to SAM depletion which is crucial to epigenetic persistence. Furthermore, this mechanism is conserved in vivo, independently of age.

It could be interesting to extend the time of treatment both in vivo and in vitro in order to see if DNA methylation is still conserved and to investigate if this response is capable of maintaining epigenetic persistence during a longer time span. It could be also interesting to explore the physiological implications of a low methionine diet in heart and liver, because these two organs were previously found to be affected by methionine levels (5). This study gave a first insight of an epigenetic response aimed at the maintenance of epigenetic persistence following metabolic stresses, hinting that similar mechanisms could also be present in different histone PTMs so as to adapt to other metabolites depletion.

References

  1. Haws, Spencer A., Deyang Yu, Cunqi Ye, Coral K. Wille, Long C. Nguyen, Kimberly A. Krautkramer, Jay L. Tomasiewicz, et al. «Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence». Molecular Cell 78, n. 2 (aprile 2020): 210-223.e8. https://doi.org/10.1016/j.molcel.2020.03.004.
  2. Etchegaray, Jean-Pierre, e Raul Mostoslavsky. «Interplay between Metabolism and Epigenetics: A Nuclear Adaptation to Environmental Changes». Molecular Cell 62, n. 5 (giugno 2016): 695–711. https://doi.org/10.1016/j.molcel.2016.05.029.
  3. Green, Cara L., e Dudley W. Lamming. «Regulation of Metabolic Health by Essential Dietary Amino Acids». Mechanisms of Ageing and Development 177 (gennaio 2019): 186–200. https://doi.org/10.1016/j.mad.2018.07.004.
  4. Lee BC, Kaya A, Gladyshev VN. Methionine restriction and life-span control. Ann N Y Acad Sci. 2016 Jan; 1363:116-24. doi: 10.1111/nyas.12973. Epub 2015 Dec 10. PMID: 26663138; PMCID: PMC5008916.
  5. Li, Z., Wang, F., Liang, B. et al.Methionine metabolism in chronic liver diseases: an update on molecular mechanism and therapeutic implication. Sig Transduct Target Ther5, 280 (2020). https://doi.org/10.1038/s41392-020-00349-7

Carlotta Valle

Master Industrial Biotechnology student

Caterina Viotto

Master Industrial Biotechnology student