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## Recent Publications

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Head of Institute: Prof. Oren Froy

Institute of Biochemistry, Food Science and Nutrition,
Robert H. Smith Faculty of Agriculture, Food and Environment,
The Hebrew University of Jerusalem,
P.O.Box 12, Rehovot 7610001, ISRAEL

Tel: +972 - (0)8-9489385
Fax: +972 - (0)8-9363208

# Publications

2017
Oren, T. ; Nimri, L. ; Yehuda-Shnaidman, E. ; Staikin, K. ; Hadar, Y. ; Friedler, A. ; Amartely, H. ; Slutzki, M. ; Di Pizio, A. ; Niv, M. Y. ; et al. Recombinant ostreolysin induces brown fat-like phenotype in HIB-1B cells. Molecular Nutrition & Food ResearchMolecular Nutrition & Food ResearchMol. Nutr. Food Res. 2017, 61, 1700057. Publisher's VersionAbstract
Scope Brown adipose tissue (BAT) is the main regulator of thermogenesis by increasing energy expenditure through the uncoupling of oxidative metabolism from ATP synthesis. There is a growing body of evidence for BAT being the key responsible organ in combating obesity and its related disorders. Herein we propose the fungal protein ostreolysin (Oly), which has been previously shown to bind to cholesterol-enriched raft-like membrane domains (lipid rafts) of mammalian cells, as a suitable candidate for interaction with brown preadipocytes. The aim of the present study was therefore to characterize the mechanism by which a recombinant version of ostreolysin (rOly) induces brown adipocyte differentiation. Methods and results Primary isolated brown preadipocytes or HIB-1B brown preadipocyte cells were treated with rOly and the effects on morphology, lipid accumulation, respiration rate, and associated gene and protein expression were measured. rOly upregulated mRNA and protein levels of factors related to brown adipocyte differentiation, induced lipid droplet formation, and increased cellular respiration rate due to expression of uncoupling protein 1. rOly also upregulated ?-tubulin expression, and therefore microtubules might be involved in its mechanism of action. Conclusion rOly promotes brown adipocyte differentiation, suggesting a new mechanism for rOly's contribution to the battle against obesity.
Argov-Argaman, N. ; Mandel, D. ; Lubetzky, R. ; Kedem, M. H. ; Cohen, B. - C. ; Berkovitz, Z. ; Reifen, R. Human milk fatty acids composition is affected by maternal age. J Matern Fetal Neonatal Med 2017, 30, 34-37.Abstract
Human colostrums and transition milk were collected from women under the age of 37 years and women aged 37 years and older. Transition milk of the younger group had lower fat content and 10-fold higher concentrations of omega 6 FA, eicosadecanoic, and arachdonic acids. Gestational age affected the colostrum concentration of total fat and omega 3 and omega 6 FA composition only in the older group. We concluded that age may be a factor in the FA composition of human milk. This should be taken into account when planning diets for pregnant women of different ages.
Bar-El Dadon, S. ; Reifen, R. Vitamin A and the epigenome. Critical Reviews in Food Science and Nutrition 2017, 57, 2404-2411. Publisher's VersionAbstract
ABSTRACTThe epigenetic phenomena refer to heritable changes in gene expression other than those in the DNA sequence, such as DNA methylation and histone modifications. Major research progress in the last few years has provided further proof that environmental factors, including diet and nutrition, can influence physiologic and pathologic processes through epigenetic alterations, which in turn influence gene expression. This influence is termed nutritional epigenetics, and one prominent example is the regulation of gene transcription by vitamin A through interaction to its nuclear receptor.Vitamin A is critical throughout life. Together with its derivatives, it regulates diverse processes including reproduction, embryogenesis, vision, growth, cellular differentiation and proliferation, maintenance of epithelial cellular integrity and immune function.Here we review the epigenetic role of vitamin A in cancer, stem cells differentiation, proliferation, and immunity. The data presented here show that retinoic acid is a potent agent capable of inducing alterations in epigenetic modifications that produce various effects on the phenotype. Medical benefits of vitamin A as an epigenetic modulator, especially with respect to its chronic use as nutritional supplement, should rely on our further understanding of its epigenetic effects during health and disease, as well as through different generations.
Wiseman, E. M. ; Bar-El Dadon, S. ; Reifen, R. The vicious cycle of vitamin a deficiency: A review. Critical Reviews in Food Science and Nutrition 2017, 57, 3703-3714. Publisher's VersionAbstract
Slutzki, M. ; Ben-Shimon, A. ; Niv, M. Y. AnchorDock for Blind Flexible Docking of Peptides to Proteins. In Modeling Peptide-Protein Interactions: Methods and Protocols; Schueler-Furman, O. ; London, N., Ed. Modeling Peptide-Protein Interactions: Methods and Protocols; Springer New York: New York, NY, 2017; pp. 95–108. Publisher's VersionAbstract
Due to increasing interest in peptides as signaling modulators and drug candidates, several methods for peptide docking to their target proteins are under active development. The blind'' docking problem, where the peptide-binding site on the protein surface is unknown, presents one of the current challenges in the field. AnchorDock protocol was developed by Ben-Shimon and Niv to address this challenge.
Cheled-Shoval, S. ; Behrens, M. ; Korb, A. ; Di Pizio, A. ; Meyerhof, W. ; Uni, Z. ; Niv, M. Y. From Cell to Beak: In-Vitro and In-Vivo Characterization of Chicken Bitter Taste Thresholds. Molecules 2017, 22.Abstract
Bitter taste elicits an aversive reaction, and is believed to protect against consuming poisons. Bitter molecules are detected by the Tas2r family of G-protein-coupled receptors, with a species-dependent number of subtypes. Chickens demonstrate bitter taste sensitivity despite having only three bitter taste receptors-ggTas2r1, ggTas2r2 and ggTas2r7. This minimalistic bitter taste system in chickens was used to determine relationships between in-vitro (measured in heterologous systems) and in-vivo (behavioral) detection thresholds. ggTas2r-selective ligands, nicotine (ggTas2r1), caffeine (ggTas2r2), erythromycin and (+)-catechin (ggTas2r7), and the Tas2r-promiscuous ligand quinine (all three ggTas2rs) were studied. Ligands of the same receptor had different in-vivo:in-vitro ratios, and the ggTas2r-promiscuous ligand did not exhibit lower in-vivo:in-vitro ratios than ggTas2r-selective ligands. In-vivo thresholds were similar or up to two orders of magnitude higher than the in-vitro ones.
Cheled-Shoval, S. L. ; Reicher, N. ; Niv, M. Y. ; Uni, Z. Detecting thresholds for bitter, umami, and sweet tastants in broiler chicken using a 2-choice test method. Poultry Science 2017, 96, 2206 - 2218. Publisher's VersionAbstract
The sense of taste has a key role in nutrient sensing and food intake in animals. A standardized and simple method for determination of tastant-detection thresholds is required for chemosensory research in poultry. We established a 24-h, 2-alternative, forced-choice solution-consumption method and applied it to measure detection thresholds for 3 G-protein-coupled receptor-mediated taste modalities—bitter, sweet, and umami—in chicken. Four parameters were used to determine a significant response: 1) tastant-solution consumption; 2) water (tasteless) consumption; 3) total consumption (tastant and water together); 4) ratio of tastant consumption to total consumption. Our results showed that assignment of the taste solutions and a water control to 2 bottles on random sides of the pen can be reliably used for broiler chicks, even though 47% of the chicks groups demonstrated a consistently preferred side. The detection thresholds for quinine (bitter), L-monosodium glutamate (MSG) (umami), and sucrose (sweet) were determined to be 0.3 mM, 300 mM, and 1 M, respectively. The threshold results for quinine were similar to those for humans and rodents, but the chicks were found to be less sensitive to sucrose and MSG. The described method is useful for studying detection thresholds for tastants that have the potential to affect feed and water consumption in chickens.
Oren, T. ; Nimri, L. ; Yehuda-Shnaidman, E. ; Staikin, K. ; Hadar, Y. ; Friedler, A. ; Amartely, H. ; Slutzki, M. ; Di Pizio, A. ; Niv, M. Y. ; et al. Recombinant ostreolysin induces brown fat-like phenotype in HIB-1B cells. Molecular Nutrition & Food Research 2017, 61, 1700057. Publisher's VersionAbstract
Scope Brown adipose tissue (BAT) is the main regulator of thermogenesis by increasing energy expenditure through the uncoupling of oxidative metabolism from ATP synthesis. There is a growing body of evidence for BAT being the key responsible organ in combating obesity and its related disorders. Herein we propose the fungal protein ostreolysin (Oly), which has been previously shown to bind to cholesterol-enriched raft-like membrane domains (lipid rafts) of mammalian cells, as a suitable candidate for interaction with brown preadipocytes. The aim of the present study was therefore to characterize the mechanism by which a recombinant version of ostreolysin (rOly) induces brown adipocyte differentiation. Methods and results Primary isolated brown preadipocytes or HIB-1B brown preadipocyte cells were treated with rOly and the effects on morphology, lipid accumulation, respiration rate, and associated gene and protein expression were measured. rOly upregulated mRNA and protein levels of factors related to brown adipocyte differentiation, induced lipid droplet formation, and increased cellular respiration rate due to expression of uncoupling protein 1. rOly also upregulated β-tubulin expression, and therefore microtubules might be involved in its mechanism of action. Conclusion rOly promotes brown adipocyte differentiation, suggesting a new mechanism for rOly's contribution to the battle against obesity.
Dubovski, N. ; Ert, E. ; Niv, M. Y. Bitter mouth-rinse affects emotions. Food Quality and Preference 2017, 60, 154 - 164. Publisher's VersionAbstract
The sense of taste enables evaluation of food and is an important regulator of food consumption. In general, sweet is an attractive taste modality that leads to ingestion of nutritive food, while sour and bitter are aversive taste modalities that lead to avoidance of spoiled and toxic food. Recent studies suggest inter-connections between taste, emotion and cognition. Here we test the potential effects of two prototypical taste modalities, bitter and sweet, on emotions and on generalized avoidance behaviors, such as risk aversion and mistrust. Three experiments included over 250 participants who tasted, without swallowing, one of the following stimuli: water control, quinine solution, sucrose solution, quinine-sucrose mixture solution, or propylthiouracil (PROP) solution. The participants had to identify the taste, rank its intensity, perform seemingly unrelated behavioral tasks, and fill a PANAS mood questionnaire. Our results indicate that oral exposure to bitter compounds negatively correlates with mood scores; that the effect depends on perceiving the solution as bitter; that bitter mouth rinse can lower PANAS mood score and that there is a potential asymmetry in the effects of bitter and sweet taste modalities on mood.
Dagan-Wiener, A. ; Nissim, I. ; Ben Abu, N. ; Borgonovo, G. ; Bassoli, A. ; Niv, M. Y. Bitter or not? BitterPredict, a tool for predicting taste from chemical structure. 2017, 7 12074. Publisher's VersionAbstract
Bitter taste is an innately aversive taste modality that is considered to protect animals from consuming toxic compounds. Yet, bitterness is not always noxious and some bitter compounds have beneficial effects on health. Hundreds of bitter compounds were reported (and are accessible via the BitterDB http://bitterdb.agri.huji.ac.il/dbbitter.php), but numerous additional bitter molecules are still unknown. The dramatic chemical diversity of bitterants makes bitterness prediction a difficult task. Here we present a machine learning classifier, BitterPredict, which predicts whether a compound is bitter or not, based on its chemical structure. BitterDB was used as the positive set, and non-bitter molecules were gathered from literature to create the negative set. Adaptive Boosting (AdaBoost), based on decision trees machine-learning algorithm was applied to molecules that were represented using physicochemical and ADME/Tox descriptors. BitterPredict correctly classifies over 80% of the compounds in the hold-out test set, and 70–90% of the compounds in three independent external sets and in sensory test validation, providing a quick and reliable tool for classifying large sets of compounds into bitter and non-bitter groups. BitterPredict suggests that about 40% of random molecules, and a large portion (66%) of clinical and experimental drugs, and of natural products (77%) are bitter.
Di Pizio, A. ; Kruetzfeldt, L. - M. ; Cheled-Shoval, S. ; Meyerhof, W. ; Behrens, M. ; Niv, M. Y. Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test-case. 2017, 7 8223. Publisher's VersionAbstract
Bitter taste is one of the basic taste modalities, warning against consuming potential poisons. Bitter compounds activate members of the bitter taste receptor (Tas2r) subfamily of G protein-coupled receptors (GPCRs). The number of functional Tas2rs is species-dependent. Chickens represent an intriguing minimalistic model, because they detect the bitter taste of structurally different molecules with merely three bitter taste receptor subtypes. We investigated the binding modes of several known agonists of a representative chicken bitter taste receptor, ggTas2r1. Because of low sequence similarity between ggTas2r1 and crystallized GPCRs (~10% identity, ~30% similarity at most), the combination of computational approaches with site-directed mutagenesis was used to characterize the agonist-bound conformation of ggTas2r1 binding site between TMs 3, 5, 6 and 7. We found that the ligand interactions with N93 in TM3 and/or N247 in TM5, combined with hydrophobic contacts, are typically involved in agonist recognition. Next, the ggTas2r1 structural model was successfully used to identify three quinine analogues (epiquinidine, ethylhydrocupreine, quinidine) as new ggTas2r1 agonists. The integrated approach validated here may be applicable to additional cases where the sequence identity of the GPCR of interest and the existing experimental structures is low.
Nissim, I. ; Dagan-Wiener, A. ; Niv, M. Y. The taste of toxicity: A quantitative analysis of bitter and toxic molecules. IUBMB Life 2017, 69, 938-946. Publisher's VersionAbstract
Abstract The role of bitter taste—one of the few basic taste modalities—is commonly assumed to signal toxicity and alert animals against consuming harmful compounds. However, it is known that some toxic compounds are not bitter and that many bitter compounds have negligible toxicity while having important health benefits. Here we apply a quantitative analysis of the chemical space to shed light on the bitterness-toxicity relationship. Using the BitterDB dataset of bitter molecules, The BitterPredict prediction tool, and datasets of toxic compounds, we quantify the identity and similarity between bitter and toxic compounds. About 60% of the bitter compounds have documented toxicity and only 56% of the toxic compounds are known or predicted to be bitter. The LD50 value distributions suggest that most of the bitter compounds are not very toxic, but there is a somewhat higher chance of toxicity for known bitter compounds compared to known nonbitter ones. Flavonoids and alpha acids are more common in the bitter dataset compared with the toxic dataset. In contrast, alkaloids are more common in the toxic datasets compared to the bitter dataset. Interestingly, no trend linking LD50 values with the number of activated bitter taste receptors (TAS2Rs) subtypes is apparent in the currently available data. This is in accord with the newly discovered expression of TAS2Rs in several extra-oral tissues, in which they might be activated by yet unknown endogenous ligands and play non-gustatory physiological roles. These results suggest that bitter taste is not a very reliable marker for toxicity, and is likely to have other physiological roles. © 2017 IUBMB Life, 69(12):938–946, 2017
Wu, C. ; Du, Y. - W. ; Huang, L. ; Ben-Shoshan Galeczki, Y. ; Dagan-Wiener, A. ; Naim, M. ; Niv, M. Y. ; Wang, P. Biomimetic Sensors for the Senses: Towards Better Understanding of Taste and Odor Sensation. Sensors (Basel) 2017, 17.Abstract
Taste and smell are very important chemical senses that provide indispensable information on food quality, potential mates and potential danger. In recent decades, much progress has been achieved regarding the underlying molecular and cellular mechanisms of taste and odor senses. Recently, biosensors have been developed for detecting odorants and tastants as well as for studying ligand-receptor interactions. This review summarizes the currently available biosensing approaches, which can be classified into two main categories: in vitro and in vivo approaches. The former is based on utilizing biological components such as taste and olfactory tissues, cells and receptors, as sensitive elements. The latter is dependent on signals recorded from animals' signaling pathways using implanted microelectrodes into living animals. Advantages and disadvantages of these two approaches, as well as differences in terms of sensing principles and applications are highlighted. The main current challenges, future trends and prospects of research in biomimetic taste and odor sensors are discussed.
Kalish-Achrai, N. ; Monsonego-Ornan, E. ; Shahar, R. Structure, composition, mechanics and growth of spines of the dorsal fin of blue tilapia Oreochromis aureus and common carp Cyprinus carpio. Journal of Fish Biology 2017, 90, 2073-2096. Publisher's VersionAbstract
The structural, compositional and mechanical properties of the spines of the dorsal fin in mature anosteocytic blue tilapia Oreochromis aureus and osteocytic common carp Cyprinus carpio are described, as well as their temporal growth pattern and regenerative capacities. The three-dimensional architecture of both spines, from macro to sub-micron levels, is shown to be axially oriented and therefore highly anisotropic and the spines of both species are able to regenerate after partial amputation.
Barazani, O. ; Waitz, Y. ; Tugendhaft, Y. ; Dorman, M. ; Dag, A. ; Hamidat, M. ; Hijawi, T. ; Kerem, Z. ; Westberg, E. ; Kadereit, J. W. Testing the potential significance of different scion/rootstock genotype combinations on the ecology of old cultivated olive trees in the southeast Mediterranean area. 2017, 17, 3. Publisher's VersionAbstract
A previous multi-locus lineage (MLL) analysis of SSR-microsatellite data of old olive trees in the southeast Mediterranean area had shown the predominance of the Souri cultivar (MLL1) among grafted trees. The MLL analysis had also identified an MLL (MLL7) that was more common among rootstocks than other MLLs. We here present a comparison of the MLL combinations MLL1 (scion)/MLL7 (rootstock) and MLL1/MLL1 in order to investigate the possible influence of rootstock on scion phenotype.
Elyasiyan, U. ; Nudel, A. ; Skalka, N. ; Rozenberg, K. ; Drori, E. ; Oppenheimer, R. ; Kerem, Z. ; Rosenzweig, T. Anti-diabetic activity of aerial parts of Sarcopoterium spinosum. 2017, 17, 356. Publisher's VersionAbstract
Sarcopoterium spinosum (S. spinosum) is used by Bedouin medicinal practitioners for the treatment of diabetes. While the anti-diabetic activity of S. spinosum root extract was validated in previous studies, the activity of aerial parts of the same plants has not been elucidated yet. The aim of this study was to clarify the glucose lowering properties of the aerial parts of the shrub.
Ehrlich, Y. ; Regev, L. ; Kerem, Z. ; Boaretto, E. Radiocarbon Dating of an Olive Tree Cross-Section: New Insights on Growth Patterns and Implications for Age Estimation of Olive Trees. Frontiers in Plant Science 2017, 8 1918. Publisher's VersionAbstract
The age of living massive olive trees is often assumed to be between hundreds and even thousands of years. These estimations are usually based on the girth of the trunk and an extrapolation based on a theoretical annual growth rate. It is difficult to objectively verify these claims, as a monumental tree may not be cut down for analysis of its cross-section. In addition, the inner and oldest part of the trunk in olive trees usually rots, precluding the possibility of carting out radiocarbon analysis of material from the first years of life of the tree. In this work we present a cross-section of an olive tree, previously estimated to be hundreds of years old, which was cut down post-mortem in 2013. The cross-section was radiocarbon dated at numerous points following the natural growth pattern, which was made possible to observe by viewing the entire cross-section. Annual growth rate values were calculated and compared between different radii. The cross-section also revealed a nearly independent segment of growth, which would clearly offset any estimations based solely on girth calculations. Multiple piths were identified, indicating the beginning of branching within the trunk. Different radii were found to have comparable growth rates, resulting in similar estimates dating the piths to the 19th century. The estimated age of the piths represent a terminus ante quem for the age of the tree, as these are piths of separate branches. However, the tree is likely not many years older than the dated piths, and certainly not centuries older. The oldest radiocarbon-datable material in this cross-section was less than 200 years old, which is in agreement with most other radiocarbon dates of internal wood from living olive trees, rarely older than 300 years.
Hayouka, Z. ; Bella, A. ; Stern, T. ; Ray, S. ; Jiang, H. ; Grovenor, C. R. M. ; Ryadnov, M. G. Binary Encoding of Random Peptide Sequences for Selective and Differential Antimicrobial Mechanisms. Angewandte Chemie International Edition 2017, 56, 8099-8103. Publisher's VersionAbstract
Abstract Binary encoding of peptide sequences into differential antimicrobial mechanisms is reported. Such sequences are random in composition, but controllable in chain length, are assembled from the same two amino acids, but differ in the stereochemistry of one. Regardless of chirality, the sequences lyse bacteria including the “superbugs” methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE). Sequences with the same chirality, so-called homochiral sequences, assemble into antimicrobial pores and form contiguous helices that are biologically promiscuous and hemolytic. By contrast, heterochiral sequences that lack such persistence selectively attack bacterial membranes without oligomerizing into visible pores. These results offer a mechanistic rationale for designing membrane-selective and sequence-independent antimicrobials.
Isaac, R. ; Goldstein, I. ; Furth, N. ; Zilber, N. ; Streim, S. ; Boura-Halfon, S. ; Elhanany, E. ; Rotter, V. ; Oren, M. ; Zick, Y. TM7SF3, a novel p53-regulated homeostatic factor, attenuates cellular stress and the subsequent induction of the unfolded protein response. 2017, 24, 132 - 143. Publisher's VersionAbstract
Earlier reported small interfering RNA (siRNA) high-throughput screens, identified seven-transmembrane superfamily member 3 (TM7SF3) as a novel inhibitor of pancreatic β-cell death. Here we show that TM7SF3 maintains protein homeostasis and promotes cell survival through attenuation of ER stress. Overexpression of TM7SF3 inhibits caspase 3/7 activation. In contrast, siRNA-mediated silencing of TM7SF3 accelerates ER stress and activation of the unfolded protein response (UPR). This involves inhibitory phosphorylation of eukaryotic translation initiation factor 2α activity and increased expression of activating transcription factor-3 (ATF3), ATF4 and C/EBP homologous protein, followed by induction of apoptosis. This process is observed both in human pancreatic islets and in a number of cell lines. Some of the effects of TM7SF3 silencing are evident both under basal conditions, in otherwise untreated cells, as well as under different stress conditions induced by thapsigargin, tunicamycin or a mixture of pro-inflammatory cytokines (tumor necrosis factor alpha, interleukin-1 beta and interferon gamma). Notably, TM7SF3 is a downstream target of p53: activation of p53 by Nutlin increases TM7SF3 expression in a time-dependent manner, although silencing of p53 abrogates this effect. Furthermore, p53 is found in physical association with the TM7SF3 promoter. Interestingly, silencing of TM7SF3 promotes p53 activity, suggesting the existence of a negative-feedback loop, whereby p53 promotes expression of TM7SF3 that acts to restrict p53 activity. Our findings implicate TM7SF3 as a novel p53-regulated pro-survival homeostatic factor that attenuates the development of cellular stress and the subsequent induction of the UPR.
Goldstein, I. ; Baek, S. ; Presman, D. M. ; Paakinaho, V. ; Swinstead, E. E. ; Hager, G. L. Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response. Genome Res 2017, 27, 427-439.Abstract
Fasting elicits transcriptional programs in hepatocytes leading to glucose and ketone production. This transcriptional program is regulated by many transcription factors (TFs). To understand how this complex network regulates the metabolic response to fasting, we aimed at isolating the enhancers and TFs dictating it. Measuring chromatin accessibility revealed that fasting massively reorganizes liver chromatin, exposing numerous fasting-induced enhancers. By utilizing computational methods in combination with dissecting enhancer features and TF cistromes, we implicated four key TFs regulating the fasting response: glucocorticoid receptor (GR), cAMP responsive element binding protein 1 (CREB1), peroxisome proliferator activated receptor alpha (PPARA), and CCAAT/enhancer binding protein beta (CEBPB). These TFs regulate fuel production by two distinctly operating modules, each controlling a separate metabolic pathway. The gluconeogenic module operates through assisted loading, whereby GR doubles the number of sites occupied by CREB1 as well as enhances CREB1 binding intensity and increases accessibility of CREB1 binding sites. Importantly, this GR-assisted CREB1 binding was enhancer-selective and did not affect all CREB1-bound enhancers. Single-molecule tracking revealed that GR increases the number and DNA residence time of a portion of chromatin-bound CREB1 molecules. These events collectively result in rapid synergistic gene expression and higher hepatic glucose production. Conversely, the ketogenic module operates via a GR-induced TF cascade, whereby PPARA levels are increased following GR activation, facilitating gradual enhancer maturation next to PPARA target genes and delayed ketogenic gene expression. Our findings reveal a complex network of enhancers and TFs that dynamically cooperate to restore homeostasis upon fasting.