Nature Metabolism

Very preterm birth disrupts critical fetal developmental programs, yet the systemic molecular trajectories driving extrauterine adaptation remain poorly defined. Although extracellular vesicles (EVs) represent informative systemic compartments, comprehensive multi-omics is constrained by the small plasma volumes safely obtainable from neonates. Here, we adapted a magnetic bead-based framework (Mag-Net) to enable parallel EV proteomics and lipidomics from the same EV-enriched preparation using 10 {micro}L of plasma. Across 74 longitudinal samples collected from birth to term-equivalent age, we quantified 1,528 EV-associated proteins and 421 lipid species. The EV proteome shifted from early translation and metabolic programs toward progressive immune competence, while the lipidome underwent selective structural remodeling enriched in triacylglycerols and ether-linked phosphatidylcholines. Cross-omics integration identified coordinated protein-lipid modules associated with clinical phenotypes, including brain injury. This study demonstrates that parallel EV proteomic-lipidomic profiling from microliter plasma volumes is feasible and captures coordinated developmental and clinically relevant programs in very preterm infants.

AbstractsGestational diabetes mellitus (GDM) is a common metabolic complication of pregnancy that is paradoxically associated with both fetal overgrowth and fetal growth restriction (FGR). While maternal hyperglycemia is widely presumed to drive macrosomia through excessive nutrient supply, the mechanisms underlying FGR remain poorly understood. Here, using a mouse model that recapitulates the small-for-gestational-age (SGA) phenotype observed in human GDM pregnancies, we identify placental underdevelopment as a principal driver of FGR. Despite systemic nutrient abundance, hyperglycemic placentas exhibit reduced mass and an increased fetal-to-placental weight ratio, indicative of placental insufficiency. Mechanistically, maternal hyperglycemia induces anabolic metabolic rewiring while suppressing oxidative phosphorylation (OXPHOS), accompanied by upregulation and nuclear redistribution of ATP-citrate lyase (ACLY). ACLY converts glucose-derived carbon into acetyl-CoA in the cytosol and nucleus, thereby coupling glycolytic flux to lipid and hexosamine biosynthesis as well as to global histone hyperacetylation. This hyperacetylation-associated epigenetic reprogramming activates metabolic, innate immune, and inflammatory gene programs while repressing pro-proliferative and anti-apoptotic pathways. Consequently, placental growth is compromised despite nutrient excess. Importantly, activation of the ACLY-acetyl-CoA axis and global histone hyperacetylation is consistently observed in human GDM placentas across diverse birth outcomes, suggesting a conserved metabolic-epigenetic adaptation to maternal hyperglycemia. Together, these findings identify ACLY-dependent acetyl-CoA production as a central metabolic node linking maternal hyperglycemia to chromatin remodeling and placental development control, thereby reshaping fetal growth trajectories.

Adaptive thermogenesis requires coordinated activation of mitochondrial oxidation and metabolic remodeling, yet the signals driving this coordination are incompletely understood. Here, we show that cold exposure and {beta}3-adrenergic receptor ({beta}3-AR) stimulation upregulate the high-affinity copper (Cu) importer CTR1 and promote Cu accumulation in thermogenic adipose tissues. Adipocyte-specific Ctr1 knockout (ACKO) mice exhibit markedly reduced energy expenditure and develop severe hypothermia during acute cold challenge. Proteomic analysis of brown adipose tissue (BAT) from ACKO mice reveals coordinated suppression of oxidative phosphorylation and thermogenic metabolic programs, accompanied by attenuation of lipolytic pathways. Cu deficiency also impairs cold- and {beta}3-AR-induced lipolytic activation, including reduced HSL phosphorylation and lipid clearance in both BAT and inguinal white adipose tissue (iWAT). Although BAT-specific Ctr1 deletion (BCKO) leaves acute {beta}3-adrenergic responses largely intact, these mice still exhibit cold intolerance, indicating that BAT Cu homeostasis is indispensable for sustaining thermogenic capacity during cold challenge. Treatment with the Cu ionophore elesclomol partially restores mitochondrial oxidative capacity and improves cold tolerance in ACKO mice. Together, these findings identify CTR1-dependent Cu import as a dynamically regulated component of the {beta}3-adrenergic thermogenic program and establish intracellular Cu availability as a key determinant of thermogenic capacity during adaptive thermogenesis.

Brown adipose tissue (BAT) exhibits exceptional metabolic plasticity, rapidly increasing energy expenditure to sustain thermogenesis during cold exposure. This high metabolic activity imposes substantial demands on cellular systems, requiring robust adaptive mechanisms to maintain homeostasis and prevent cellular stress. Yet, the pathways that support and coordinate these adaptive responses in brown adipocytes remain incompletely understood. Here, we identify a cold-induced adaptive program in BAT characterized by the formation of endoplasmic reticulum-plasma membrane (ER-PM) contact sites and the activation of store-operated calcium entry (SOCE), which is essential for maintaining brown adipocyte health during thermogenic activation. Cold exposure enhances ER-PM contacts and upregulates the expression of STIM and Orai proteins, key mediators of SOCE. Loss of STIM in brown adipocytes disrupts intracellular Ca{superscript 2} homeostasis and induces aberrant aggregation of ER membranes. STIM deficiency also impairs cold-induced mitochondrial fission resulting in hyperfused mitochondria with reduced oxidative capacity, independently of UCP1 abundance. Importantly, mice lacking STIM in BAT exhibit impaired lipid oxidation, are cold intolerant and develop exacerbated peripheral insulin resistance when challenged with a high-fat diet. Together, these findings identify ER-PM remodeling and STIM-mediated SOCE as a central regulator that links organelle architecture to brown adipocyte function and contributes to whole-body metabolic homeostasis.

The gut microbiota produces metabolites that circulate to host tissues and are increasingly linked to metabolic health, yet the mechanisms by which individual microbial products regulate liver glucose metabolism remain poorly defined. Here, we identify the tryptophan-derived microbial metabolite indole-3-propionic acid (IPA) as a direct modulator of hepatic glucose production. In primary hepatocytes, a focused screen of indole metabolites revealed that several indole-containing compounds suppress glucagon-stimulated glucose output, with IPA emerging as a physiologically relevant candidate. IPA selectively reduced glucose production from mitochondrial-dependent gluconeogenic substrates while largely preserving glycerol-supported glucose production, suggesting that it does not simply shut down gluconeogenesis but instead alters how hepatocytes use metabolic fuels. Mechanistic analyses showed that IPA redirects lactate-derived carbon away from glucose production and reshapes mitochondrial metabolism, including redox balance, ATP availability, and urea cycle-linked metabolic activity. These effects occurred without detectable disruption of proximal insulin or glucagon signaling, supporting a model in which IPA acts primarily through intracellular metabolic remodeling. In mice, endogenous IPA levels varied with nutritional state, and short-term IPA administration improved fasting glycemia and glucose handling in Western diet-fed animals. Finally, microbiome-depleted mice colonized with IPA-producing Clostridium sporogenes displayed increased circulating IPA and improved glucose tolerance compared with mice colonized with an IPA-deficient mutant C. Sporogenes strain. Together, these findings identify IPA as a microbial metabolite that directly connects gut tryptophan metabolism to hepatic mitochondrial function and systemic glucose regulation, highlighting a mechanistic gut-liver pathway with potential therapeutic relevance to metabolic disease.

Severe hypoglycemia remains a serious adverse effect of insulin therapy in individuals with diabetes and is linked to cognitive decline, yet the mechanisms by which transient metabolic stress leads to persistent neuronal dysfunction remain poorly defined. Using mouse models of acute severe hypoglycemia and integrated screening, we identified the retrosplenial cortex as a previously unrecognized brain region that is particularly vulnerable to hypoglycemia-induced neuronal damage. This injury is driven by a feedforward interaction between neuron-specific Drp1-dependent mitochondrial fission and microglial IL-1 signaling, as pharmacological or genetic targeting of either pathway suppressed the other, rescued neuronal damage, and reversed cognitive impairment. These findings identify a region-specific neuron-microglia injury circuit that links severe hypoglycemia to cognitive dysfunction and suggest a therapeutic strategy to protect brain function without compromising diabetes management.

Interest in fasting-based dietary interventions to improve metabolic health is growing. Caloric restriction (CR) with one meal per day includes an extended fasting component that contributes to its metabolic and longevity benefits, yet the specific role of fasting within CR remains unclear. Here, we compared mice under CR with those subjected to a fasting-refeeding-fasting (FRF) regimen while controlling pre-fasting food intake and fasting duration. Simultaneous comparison of diet induced changes in plasma insulin and free fatty acids, hepatic mTOR signaling and ketogenesis, total body metabolic rhythms with kinetics of food digestion suggested that gastric emptying served as a primary metabolic trigger in acute fasting. In contrast, in CR, fasting responses were actively regulated and suggested anticipatory mechanisms. At the transcriptomic level, CR enhanced circadian rhythmicity and metabolic gene coordination, whereas FRF disrupted it. In agreement with the expression data, CR improves glucose and fatty acid metabolism while fasting leads to glucose intolerance and fat accumulation in the liver induced glucose intolerance and hepatic steatosis. These findings reveal that CR engages clock-aligned, anticipatory metabolic control, while fasting-refeeding cycles rely on direct nutrient cues. This mechanistic distinction between active and passive metabolic regulation may underlie the superior metabolic and longevity outcomes of caloric restriction.

Propionic acidemia (PA) is an inborn error of metabolism caused by propionyl-CoA carboxylase (PCC) deficiency due to mutations in either PCCA or PCCB. Without proper management, the disease is associated with high mortality. Even with dietary restriction, patients often develop complications later in life, and the underlying pathological mechanisms remain poorly understood. The liver is the primary organ responsible for propionyl-CoA metabolism, yet the metabolic alterations induced by PCC deficiency in the liver have not been systematically investigated. In this study, we used a hepatocyte model of PA-- PCCAnull-HepG2 cells--to comprehensively examine metabolic alterations using stable isotope-based metabolic flux analysis. The PCCA knockout recapitulated key metabolic features of PA in HepG2 cells. Furthermore, PCCA deficiency reduced mitochondrial fatty acid oxidation while increasing glucose oxidation through pyruvate dehydrogenase. In contrast, pyruvate anaplerosis via pyruvate carboxylase was markedly reduced in PCCA knockout cells. This reduction in anaplerotic flux impaired the capacity for gluconeogenesis and lipid synthesis, consistent with observations from in vivo studies in Pcca-/- (A138T) mice. Additionally, branched-chain keto acid catabolism was reduced in PCCA knockout HepG2 cells. Threonine showed minimal metabolic contribution in this model, further supporting the role of propionate as a major source of propionyl-CoA production. Collectively, these findings highlight the metabolic vulnerabilities associated with PCC deficiency and underscore the increased risk of prolonged fasting in patients with PA, particularly those with severe disease.

Maternal nutrition shapes offspring brain development and influences lifelong risk for neurological disorders, yet the circuit-level mechanisms linking maternal metabolic state to offspring behavior remain poorly defined. Here we show that maternal high-fat diet (mHFD) disrupts microglia-serotonin interactions during a critical postnatal window to drive persistent, sex-specific alterations in mesolimbic circuitry. In mice, mHFD selectively increased serotonergic fiber density in the nucleus accumbens (NAc) of male, but not female, offspring at postnatal day 14, coincident with reduced microglial phagocytosis of serotonin (5-HT) projections. This early-life hyperinnervation persisted into adulthood, where male offspring exhibited elevated NAc 5-HT release and projection-specific changes in dorsal raphe neuron activity. Functionally, these circuit alterations were associated with accelerated reward-motivated learning, a phenotype recapitulated by chemogenetic activation of NAc-projecting 5-HT neurons. Together, these findings reveal a microglia-centric mechanism by which maternal diet programs serotonergic circuit assembly and behavior in a sex-specific manner, providing a potential link between early-life metabolic inflammation and lifelong neural function.

Beige adipocytes that emerge during the peri-weaning period support sympathetic nervous system (SNS)-independent thermogenesis, yet the mechanisms governing this spontaneous beiging remain unclear. Here, by integrating transcriptomic profiling with adipocyte-targeted Ctnnb1 deletion in mice, we identify the canonical Wnt signaling as an endogenous brake on developmental beige thermogenesis. Peri-weaning inguinal fat from adipocyte Ctnnb1 knockout mice exhibits enhanced beige adipocyte biogenesis, with increased thermogenesis-related gene expression and mitochondrial oxidative capacity, which programs durable activation of adaptive thermogenesis and augmented whole-body energy expenditure into adulthood. Mechanistically, suppression of Wnt/{beta}-catenin signaling induces a non-canonical Wnt5a-Ca2-AMPK axis that promotes triglyceride lipolysis and subsequent PPAR-driven fatty acid oxidation, thereby fueling mitochondrial respiration. Genetic or pharmacological disruption of this axis blunts thermogenic responses induced by {beta}-catenin inhibition in both murine and human subcutaneous adipocytes, indicating that Wnt5a-Ca2-AMPK axis is required for the cell-autonomous activation of beige fat. These results reveal Wnt/{beta}-catenin signaling as a developmental constraint on beige adipocyte formation and suggest an SNS-independent route to sustainably raise energy expenditure and improve metabolic health.

Type 2 diabetes (T2D) and cardiovascular disease are major global health burdens. Branched-chain amino acid (BCAA) metabolism has been implicated as a potential therapeutic target, but it remains unclear whether its associations with disease risk are independent of traditional risk factors such as obesity and dyslipidemia. We leveraged genomic structural equation modeling of large-scale genome-wide association studies (GWAS) from European and East Asian populations, including the largest East Asian GWAS of BCAA levels (n = 42,826). We identified a genetic factor influencing BCAA metabolism independently of body mass index and circulating lipid levels. A cross-population polygenic score derived from this factor was associated with hemoglobin A1c, blood glucose, and the onset of both T2D and coronary artery disease. These findings provide the first genetic insight in humans that BCAA metabolism is involved in T2D and CAD beyond traditional risk factors, highlighting its clinical relevance and therapeutic potential.

Daily light-dark cycles impose predictable environmental fluctuations that require coordinated temporal regulation of cellular physiology. This coordination is mediated by the circadian clock, which operates as a network of tissue oscillators; however, the molecular signals that convey circadian information between organs remain incompletely defined. Here, we identify nicotinic acid riboside (NaR) as a circulating metabolite whose rhythmicity depends on the liver clock. In differentiating 3T3-L1 adipocytes, NaR engages unfolded protein response (UPR) gene programs and modulates adipogenic competence. Proteome-wide stability profiling implicates the prefoldin complex as a molecular target of NaR signaling, linking NaR exposure to altered proteostasis. Functionally, NaR-induced UPR signaling converges on the adipogenic transcription factor CEBPA, which is a central regulator of adipogenesis. Importantly, sustained NaR exposure suppresses adipocyte lipid deposition, whereas temporally restricted NaR stimulation enhances adipogenesis, indicating that NaR acts in a time-dependent manner. Together, these findings identify NaR as a liver clock-controlled circulating metabolite that couples systemic circadian metabolism to adipocyte proteostasis and differentiation, revealing a mechanism by which temporal metabolic signals shape tissue-specific physiological outcomes. HighlightsO_LIThe circadian clock is required for rhythmic regulation of circulating nicotinic acid riboside (NaR). C_LIO_LIThe liver clock is sufficient to generate NaR rhythmicity. C_LIO_LINaR engages the prefoldin complex to regulate unfolded protein response signaling and Cebpa expression. C_LIO_LITime-dependent NaR exposure differentially regulates CEBPA levels and adipocyte lipid deposition. C_LI

Type 2 diabetes and prediabetes affect hundreds of millions of people globally, yet the metabolic networks underlying disease development remain poorly understood. Using untargeted liquid chromatography-mass spectrometry (LC-MS/MS), we profiled a total of 15,470 (900 known) serum metabolite features across the human diabetes spectrum (the most comprehensive coverage reported to date). Weighted coexpression network analysis of samples from people with normal glucose tolerance, prediabetes, and type 2 diabetes, collected at baseline and 2 hours after an oral glucose tolerance test, revealed tightly coregulated modules strongly associated with glycemic dysregulation, insulin resistance, and islet dysfunction. Notably, short-chain organic acids, particularly crotonic acid, emerged as hubs of the diabetes-associated networks, accumulating progressively with disease severity. Reanalysis of extracellular vesicle proteomics from the same cohort showed that 16.5% of circulating proteins were crotonylated, with approximately 40% correlated with crotonic acid and other hub metabolites, establishing a metabolome-crotonylome axis as a novel mechanism in diabetes development.

Pet dogs share human-like environments while aging on a compressed timescale, making them a powerful translational model for aging research. Using genomic and phenotypic data from 7,627 dogs in the Dog Aging Project, including 976 profiled for 159 blood metabolites and clinical analytes, we generated the first GWAS catalog in dogs. Blood traits map to orthologous loci in dogs and humans, indicating deeply conserved pathways. Breed ancestry explains substantial variance in blood traits, and selection on visible characteristics such as fur type has pleiotropic metabolic effects. Leveraging mosaic ancestry in mixed-breed dogs and longitudinal mortality data, we identify blood traits elevated in short-lived breeds that predict individual mortality risk -- including globulin and potassium -- and protective traits enriched in long-lived breeds, such as ethanolamine. Although some aging-associated traits relate to growth hormone pathways, many do not, indicating that aging in dogs is multifactorial. These findings establish dogs as a translational system for identifying genetic determinants and biomarkers of aging relevant to extending healthy lifespans.

Glucose is the brains primary fuel, but the brain can also use alternative energy substrates, especially during development or starvation. Emerging evidence suggests ketone metabolism may help the brain adapt to energy stress in neurodegenerative diseases such as Alzheimers disease, although its role in constitutive brain function in normal aging is poorly understood. Using iPSC-derived human neurons and adult-inducible, neuron-specific Bdh1 knockout mice, we show that ketone body metabolism is essential for maximum energy production, neuronal function, and mouse survival--even under normal nutritional conditions. Mechanistically, phenotypes of Bdh1 knockout neurons are mitigated by provision of acetoacetate, a downstream energy metabolite. Moreover, loss of neuronal ketone oxidation markedly increases mortality and memory deficits in Alzheimers disease model mice. These findings identify ketones as critical neuronal fuels, with particular importance during neurodegeneration. While non-energetic activities of ketone bodies are increasingly appreciated, oxidation for energy provision is an essential mechanism for normal function in neurons and mice. Targeting the energetic function of ketones may thus offer new therapeutic strategies for both aging and neurodegenerative diseases such as Alzheimers.

In both type 1 and type 2 diabetes (T1D and T2D), insulin-producing {beta} cells undergo progressive dysfunction due to inflammation, leading to impaired glucose responsiveness, dedifferentiation, and cell loss. While bile acid (BA) dysregulation under diabetic conditions is known to influence metabolic and inflammatory pathways, its mechanistic role in {beta} cell regulation remains incompletely defined1-3. Here we show that bile acid sensor Farnesoid X receptor (FXR) and Bromodomain and Extra-Terminal motif (BET) signaling cooperatively regulates {beta} cell inflammatory response and {beta} cell identity. We identified the physiological protein-protein interaction between FXR and the bromodomain-containing protein 4 (BRD4) as a regulatory axis that protects against {beta} cell dysfunction. We show that FXR activation by Fexaramine (Fex) together with BRD4 inhibition by JQ1 synergistically suppressed IL-1{beta}-induced inflammation while also improving {beta} cell identity and insulin secretion in both db/db model and high-fat diet (HFD) plus multi low-dose streptozotocin (MLD-STZ) model of diabetes. Importantly, this cooperative effect is abolished in {beta} cell-specific FXR knockout ({beta}FXRKO) mice, establishing that FXR is required for the functional synergy between these pathways in vivo. Mechanistically, structure-guided modeling and mutational analyses identified a direct interaction between FXR and the BD2 domain of BRD4, depending on specific lysine acetylation sites. Additionally, inhibition of the BD2 domain of BET combined with FXR activation markedly improved {beta} cell survival in human T1D and T2D models established from human pluripotent stem cell (hPSC)-derived islet-like organoids (HILOs). Collectively, these findings establish a BA-bromodomain axis as a transcriptional interface linking metabolic signaling and chromatin regulation, and highlight FXR-BET targeting as a promising strategy to counter progressive {beta} cell failure in diabetes.

Daily hepatic mitochondrial rhythms are strengthened by time-restricted feeding in diet-induced obesity in male mice, as shown by metabolomics, including an early enhancement of oscillations within the de novo pyrimidine pathway. We tested whether timed inhibition of dihydroorotate dehydrogenase (DHODH, which links pyrimidine synthesis to respiratory-chain flux), can reproduce selected TRF-associated mitochondrial and metabolic effects. Administering the short-half-life inhibitor BAY2402234 at dawn transiently decreased DHODH activity, restored daily mitochondrial oxidative dynamics (ubiquinone/ubiquinol ratio), and amplified rhythms of respiratory exchange ratio and mitochondrial dynamics-related markers upon high-fat diet. Under ZT0 dosing, mice showed reduced weight gain, reduced adiposity and hepatic triglycerides, and improved glucose tolerance without changes in food intake; while ZT12 dosing was ineffective. Hepatic Dhodh knockdown did not reproduce the anti-obesity phenotype, and uridine supplementation blunted BAY2402234 benefits, implicating de novo pyrimidine flux. Our findings reveal rhythm-aware DHODH inhibition as a chronopharmacological preclinical candidate approach against overnutrition.

Acquisition and extinction of drug-context associations both involve learning, yet whether extinction erases the original drug memory remains unresolved. As learning is associated with epigenetically mediated transcriptional plasticity, we asked whether acquisition-induced DNA methylation and gene expression changes are reversed by extinction, or whether extinction induces its own distinct methylation and transcriptional changes. Here, we show that both acquisition and extinction of cocaine conditioned place preference (CPP) preferentially hypomethylated cis-regulatory elements and upregulated transcription, but at largely non-overlapping genomic regions and genes in the dorsal dentate gyrus, a key region in contextual learning. In both learning paradigms, the number of differentially expressed genes was an order of magnitude smaller than those differentially methylated, highlighting the robustness of the transcriptional network to epigenetic modifications, and implicating a non-linear relationship between regulatory elements and transcription characteristic for gene regulatory networks (GRNs). Notably, animals that failed to extinguish cocaine CPP displayed attenuated DNA methylation changes and minimal transcriptional response, consistent with the stochastic output of GRNs to produce alternative outcomes across individuals. Acquisition-upregulated genes were enriched in neuronal cilium functions, consistent with the known role of primary cilia in hippocampal learning and the persistence of drug-context memories through stable axo-ciliary signaling. In contrast, extinction-upregulated genes were overrepresented in mitochondrial energy homeostasis functions, suggesting their role in meeting rapid energy demands during learning. Overall, acquisition and extinction engage fundamentally distinct molecular mechanisms, providing a potential mechanistic explanation for why drug-context memories are suppressed but not erased by extinction.

High-fat diet (HFD) consumption engages reward circuitry and promotes neuroadaptations that contribute to overeating and obesity. While mesolimbic dopamine pathways are central to hedonic feeding models, the contribution of sensory cortical systems remains poorly understood. Here, we performed whole-brain activity mapping using Targeted Recombination in Active Populations (TRAP) and network analysis to define the distributed neural consequences of short-term HFD exposure in male and female mice. HFD increased caloric intake in both sexes, with females consuming significantly more than males. Brain-wide analysis revealed striking sex-specific adaptations: HFD selectively increased isocortical activity in males, with the somatosensory cortex (SS) emerging as the most prominently modulated region. SS activity negatively correlated with HFD intake, primarily in males. Network analysis using the SMARTTR pipeline demonstrated that HFD reorganized network activity in a sex-dependent manner, biasing male networks toward associative cortical-thalamic hubs, whereas female networks preferentially recruited subcortical and brainstem structures. To determine causality, we bidirectionally manipulated SS pyramidal neurons using chemogenetics during limited-access HFD exposure. Inhibition of the SS increased HFD intake in males, whereas activation reduced cumulative intake in females, without affecting locomotion. These findings establish the SS as a sex-specific regulator of palatable food consumption and demonstrate that similar behavioral outcomes emerge from distinct circuit architectures across sexes. Collectively, this study expands prevailing reward-centric models of hedonic feeding by identifying sensory cortical control as a critical component of diet-induced neuroadaptations, with important implications for sex-specific therapeutic strategies targeting overeating and obesity.

Environmental exposures can influence offspring health through epigenetic alterations in the male germline. Folate deficiency, a dietary perturbation that disrupts one-carbon metabolism and S-adenosylmethionine (SAM) production, has been linked to altered histone methylation and developmental abnormalities in offspring. However, when and how folate availability shapes the germline epigenome during spermatogenesis remains unclear. In this study, unbiased metabolomic profiling of spermatogenic cells uncovers stage-specific metabolic remodeling, including downregulation of serine- glycine-one-carbon (SGOC) metabolism in meiotic spermatocytes. Using a post-weaning folate-deficient mouse model, we investigate how folate availability influences germline epigenome establishment during spermatogenesis. Consistent with this metabolic transition, genome-wide chromatin accessibility profiling demonstrates extensive, stage-dependent remodeling under folate-deficient conditions, particularly in meiotic spermatocytes and post-meiotic spermatids. These accessibility changes display cell-type-specific genomic distributions and preferential localization to repressive chromatin compartments in post-meiotic cells. Histone modification analyses further reveal bidirectional redistribution of the active histone mark H3K4me3 in round spermatids. Although genome-wide distribution of the repressive mark H3K27me3 remains largely stable, folate deficiency alters its nuclear organization. Notably, a subset of H3K4me3 alterations established in post-meiotic cells is retained in mature sperm, providing a mechanistic link between paternal metabolic perturbation and the germline epigenome. Together, these findings demonstrate that folate availability shapes germline epigenome establishment through stage-specific metabolic and chromatin remodeling during spermatogenesis, revealing a metabolic basis for paternal environmental effects on the germline epigenome.