Periodic Reporting for period 3 - MemoChrom (Adaptation to Recurring Fasting by Chromatin-Mediated Memory)
Okres sprawozdawczy: 2024-02-01 do 2025-07-31
Adaptation to recurring environmental challenges (food availability, seasonal rhythms etc.) is a mainstay of physiology. As such, mammals are exquisitely fitted to tolerate frequent bouts of fasting owing to hepatic production of fuels (glucose, ketones). This project employs nutrigenomic approaches to unravel the mechanisms behind this adaptation.
The field of nutrigenomics deals with the interplay between food, the nutritional status of the body and the genome. It focuses on the molecular level to gain insights as to how dietary regimes may affect human health. The liver is a central organ in responding to altered nutritional status. After a meal, the liver converts the absorbed carbohydrates and fats into large storage molecules. In times of lack of food (such as fasting and starvation), the liver utilizes storage molecules to supply the body with available energy sources such as sugar and alternative fuels. Many of the liver’s functions are mediated by changes in the level of gene expression, namely the amount certain genes are expressed into active proteins. Following fasting, the expression of hundreds of genes is changed to exert the metabolic role of the liver during fasting. In our previous research, we found that fasting changes the fundamental structure of DNA packaging in the liver (termed ‘chromatin’) to enable altered gene expression via cooperation between special regulatory proteins that bind DNA termed ‘transcription factors’.
Many studies show significant health benefits of intermittent fasting. Due to the reliance of the fasting response on chromatin and transcriptional regulation, we hypothesize that mammals adapt to recurring fasting by sensitizing transcriptional programs and maximizing future responses, thereby increasing survival. This project aims to uncover transcriptional mechanisms of ‘fasting memory’ that mediate the health benefits of recurrent fasting. We profile hepatic gene expression and genome-wide chromatin landscape of intermittently-fasted mice to discover the mediators of such memory. In addition, the molecular mechanisms mediating memory are examined in a series of gain/loss of function experiments targeting various components of transcriptional regulation (transcription factors, RNA polymerase, histone and DNA modifications etc.).
The field of nutrigenomics deals with the interplay between food, the nutritional status of the body and the genome. It focuses on the molecular level to gain insights as to how dietary regimes may affect human health. The liver is a central organ in responding to altered nutritional status. After a meal, the liver converts the absorbed carbohydrates and fats into large storage molecules. In times of lack of food (such as fasting and starvation), the liver utilizes storage molecules to supply the body with available energy sources such as sugar and alternative fuels. Many of the liver’s functions are mediated by changes in the level of gene expression, namely the amount certain genes are expressed into active proteins. Following fasting, the expression of hundreds of genes is changed to exert the metabolic role of the liver during fasting. In our previous research, we found that fasting changes the fundamental structure of DNA packaging in the liver (termed ‘chromatin’) to enable altered gene expression via cooperation between special regulatory proteins that bind DNA termed ‘transcription factors’.
Many studies show significant health benefits of intermittent fasting. Due to the reliance of the fasting response on chromatin and transcriptional regulation, we hypothesize that mammals adapt to recurring fasting by sensitizing transcriptional programs and maximizing future responses, thereby increasing survival. This project aims to uncover transcriptional mechanisms of ‘fasting memory’ that mediate the health benefits of recurrent fasting. We profile hepatic gene expression and genome-wide chromatin landscape of intermittently-fasted mice to discover the mediators of such memory. In addition, the molecular mechanisms mediating memory are examined in a series of gain/loss of function experiments targeting various components of transcriptional regulation (transcription factors, RNA polymerase, histone and DNA modifications etc.).
In this ERC project, we revealed a mechanism for integrating hormonal signals in liver cells, leading to an augmented metabolic response to fasting. We examined the crosstalk between the two major fasting hormones – glucagon and glucocorticoids. Each hormone was previously shown to regulate gene expression by activating transcription factors (glucagon activates CREB and glucocorticoids activate GR), but how these transcription factors crosstalk was undefined. In a paper we published, we found that following hormonal activation, these factors synergistically induce a set of genes important to glucose production. This synergistic gene induction is mediated by cooperative transcription factor binding at enhancers termed ‘assisted loading’. CREB assists the loading of GR on a subset of enhancers through increasing enhancer activity. We showed that CREB activation leads to an increase in the number, intensity and accessibility of GR binding sites, thus facilitating synergistic gene expression and increased glucose production. Thus, this work unraveled critical regulatory mechanisms at play in the liver during fasting.
In addition to this published project, we published an additional paper focusing on the characterization of chromatin accessibility. Chromatin is a DNA-protein structure that enables DNA packaging. Regions in DNA that are transcribed as well as DNA regulatory elements are packaged less densely and are termed ‘accessible’. Because our ERC project heavily relies on genome-wide profiling of chromatin accessibility, we have put significant efforts into improving and optimizing existing protocols to accommodate the special characteristics of liver tissue. Our method was recently published in a peer-reviewed journal.
The third paper from this project explored another key regulatory paradigm: transcriptional cascades. We discovered that fasting induces a network of TFs that, in turn, activate a secondary wave of gene expression. These cascades amplify the gluconeogenic response and also initiate a program that enhances ketogenesis. Our work highlights the importance of these cascades in mediating the body’s acute response to fasting and opens new avenues for studying similar cascades in other physiological processes.
In another paper from the project, we examined the response to refeeding following a period of fasting. When food is consumed again after a period of fasting (i.e. refeeding), a metabolic switch occurs and tissues transition from frugal energy usage and the internal production of fuel to using energy available from food constituents and storage of excess energy in specialized molecules. We found distinct, temporally-organized transcriptional programs occurring upon refeeding with an early wave of transcription followed by a later wave. These programs were driven by enhancer activation that also showed kinetic behavior. We showed that a lipogenic gene program is part of the second wave of transcription and is directly regulated by a TF termed liver X receptor α (LXRα). Interestingly, lipogenesis genes and their associated enhancers markedly overshoot above pre-fasting levels and this is dictated by LXRα. These findings unravel the mechanism behind the long-known phenomenon of refeeding ‘fat overshoot’.
In a recently-published paper, we found that mice undergoing alternate-day fasting (ADF) respond profoundly differently to a following fasting bout compared to mice first experiencing fasting. Hundreds of genes enabling ketogenesis are ‘sensitized’. Liver enhancers regulating these genes are also sensitized and harbor increased binding of PPARα, the main ketogenic transcription factor. ADF leads to augmented ketogenesis compared to a single fasting bout in wild-type, but not hepatocyte-specific PPARα-deficient mice. Thus, we found that past fasting events are ‘remembered’ in hepatocytes, sensitizing their enhancers to the next fasting bout and augment ketogenesis.
In addition to this published project, we published an additional paper focusing on the characterization of chromatin accessibility. Chromatin is a DNA-protein structure that enables DNA packaging. Regions in DNA that are transcribed as well as DNA regulatory elements are packaged less densely and are termed ‘accessible’. Because our ERC project heavily relies on genome-wide profiling of chromatin accessibility, we have put significant efforts into improving and optimizing existing protocols to accommodate the special characteristics of liver tissue. Our method was recently published in a peer-reviewed journal.
The third paper from this project explored another key regulatory paradigm: transcriptional cascades. We discovered that fasting induces a network of TFs that, in turn, activate a secondary wave of gene expression. These cascades amplify the gluconeogenic response and also initiate a program that enhances ketogenesis. Our work highlights the importance of these cascades in mediating the body’s acute response to fasting and opens new avenues for studying similar cascades in other physiological processes.
In another paper from the project, we examined the response to refeeding following a period of fasting. When food is consumed again after a period of fasting (i.e. refeeding), a metabolic switch occurs and tissues transition from frugal energy usage and the internal production of fuel to using energy available from food constituents and storage of excess energy in specialized molecules. We found distinct, temporally-organized transcriptional programs occurring upon refeeding with an early wave of transcription followed by a later wave. These programs were driven by enhancer activation that also showed kinetic behavior. We showed that a lipogenic gene program is part of the second wave of transcription and is directly regulated by a TF termed liver X receptor α (LXRα). Interestingly, lipogenesis genes and their associated enhancers markedly overshoot above pre-fasting levels and this is dictated by LXRα. These findings unravel the mechanism behind the long-known phenomenon of refeeding ‘fat overshoot’.
In a recently-published paper, we found that mice undergoing alternate-day fasting (ADF) respond profoundly differently to a following fasting bout compared to mice first experiencing fasting. Hundreds of genes enabling ketogenesis are ‘sensitized’. Liver enhancers regulating these genes are also sensitized and harbor increased binding of PPARα, the main ketogenic transcription factor. ADF leads to augmented ketogenesis compared to a single fasting bout in wild-type, but not hepatocyte-specific PPARα-deficient mice. Thus, we found that past fasting events are ‘remembered’ in hepatocytes, sensitizing their enhancers to the next fasting bout and augment ketogenesis.
The concepts raised here have the potential to unravel a fundamental homeostatic response and significantly advance fasting research. The gene expression networks regulating systemic metabolism in response to diet are dysregulated during diabetes and obesity and contribute to their pathogenesis. Therefore, modulation of these networks has a therapeutic potential. This project uncovered novel regulatory mechanisms that govern the body’s response to fasting, refeeding and intermittent fasting. From cooperative transcription factor dynamics to transcriptional cascades and enhancer “memory,” our work is redefining how we understand metabolic adaptation and cellular response to nutritional cues. These discoveries have not only advanced our understanding of liver biology but also provided new insights into broader principles of gene regulation that are relevant to various physiological and pathological processes.