HACS————HACS|导读：
metabolism has emerged as a node governing cellular behaviour.
Metabolic pathways fuel cellular energy needs, providing basic chemical molecules to sustain cellular homeostasis, proliferation and function.
Changes in nutrient consumption or availability therefore can result in complete reprogramming of cellular metabolism towards stabilizing core metabolite pools, such as ATP, S-adenosyl methionine, acetyl-CoA, NAD/NADP and α-ketoglutarate.
Because these metabolites underlie a variety of essential metabolic reactions, metabolism has evolved to operate in separate subcellular compartments through diversification/variety of metabolic enzyme complexes, oscillating metabolic activity and physical separation of metabolite pools.
oscillate[ˈɑːsɪleɪt] If an object oscillates, it moves repeatedly from one position to another and back again, or keeps getting bigger and smaller.
Given that these same core metabolites are also consumed by chromatin modifiers in the establishment of epigenetic signatures, metabolite consumption on and (metabolite) release from chromatin directly influence cellular metabolism and gene expression.
In this Review, we highlight recent studies describing the mechanisms determining nuclear metabolism and governing the redistribution of metabolites between the nuclear and non-nuclear compartments.
|核心内容：
Cellular metabolism supports every biological activity within the cell.
Metabolic pathways are responsible for the conversion of extracellular nutrients such as glucose, fatty acids, amino acids and vitamins into a wide range of intracellular metabolites.
These basic biochemical components can then be combined into complex macromolecules (anabolism) or broken down for the generation of energy and reducing power (catabolism).
Because metabolic pathways are highly intersectional, metabolic conversions must be compartmentalized in subcellular locations.
Metabolic compartmentalization can be obtained through：
the formation of local enzyme complexes; （生发中心germinal center）
temporal separation of reactions;
controlled influx and efflux of metabolites into isolated organelles, such as the mitochondria, Golgi apparatus and peroxisomes.
However, given the inability of the nuclear pores to prevent the passage of metabolites, the nucleus has long been considered to be in metabolic homeostasis with the cytoplasm.
然而，由于核孔无法阻止代谢物的通过，细胞核长期以来被认为与细胞质处于代谢稳态。
Nevertheless, the establishment of the so-called epigenetic code through the chemical modification of chromatin is dependent on the same core metabolites that form the basis of cellular metabolism.
Because chromatin modifications are crucial to the maintenance of cellular identity and function, mechanisms regulating nuclear metabolite pools are expected to exist.
In this Review, we provide a framework to understand the interaction of cellular and nuclear metabolism, with an emphasis on the nodal metabolites that regulate central carbon metabolism and the epigenome.
We give an overview of mechanisms that shield the epigenetic regulation of gene expression from fluctuations in cytoplasmic metabolite levels and discuss the controlled exchange in metabolites between the nuclear and non-nuclear compartments.
Finally, we propose that disruption of the nuclear metabolite pools may underlie disease.
● Metabolic pathways are reprogrammed to meet different cellular needs ●
Despite the enormous complexity of the metabolic network, a few nodal metabolites intersect in most biochemical reactions.
intersect[ˌɪntəˈsekt] If two or more lines or roads intersect, they meet or cross each other. You can also say that one line or road intersects another.
Whereas biosynthesis relies on linking one-carbon units—such as 5,10-methylenetetrahydrofolate and S-adenosyl methionine (SAMe)—with the two-carbon unit acetyl-CoA, / thermodynamically unfavourable reactions are facilitated through cellular energy and reducing power stored in the forms of ATP, NADH and NADPH.
热力学上不适宜的反应（非自发的）是通过细胞能量（ATP、NADH和NADPH）来促进的，而生物合成依赖于将单碳单位-如5，10-甲基四氢叶酸和S-腺苷甲硫氨酸(SAMe)-与双碳单位乙酰辅酶A连接起来。
Changing cellular needs（cellular change） thus require metabolic reprogramming to increase or decrease the generation of these specific metabolites.
One of the best-studied metabolic adaptations is the acquisition of aerobic glycolysis, better known as the 'Warburg effect’.
In 1857, Louis Pasteur implicated oxygen levels in determining the distribution of glucose metabolism between cytoplasmic glycolysis (anaerobic[ˌænəˈroʊbɪk] fermentation) and mitochondrial oxidation (aerobic[eˈroʊbɪk] respiration).
However, in the 1920s, Otto Warburg found that proliferating cancer cells increase the glycolytic conversion of glucose to lactate, even in the presence of sufficient amounts of oxygen, thereby linking metabolic remodelling to cellular demands. (more lactate for proliferation)
The metabolism of non-proliferating cells is aimed at the efficient generation of ATP.
Fig. 1 | Metabolic fluxes are redirected to replenish core metabolites.
replenish[rɪˈplenɪʃ] If you replenish something, you make it full or complete again. ~ (plenty of?)
Despite the enormous complexity and interconnection of the metabolic network, a few core metabolites act as basic compounds or cofactors that direct major metabolic fluxes.
For cellular maintenance, central carbon metabolism is directed at the complete oxidation of glucose into ATP (dark-blue dashed box).
In contrast, proliferating cells (red dashed box) mainly require the replenishment of molecular building blocks (分子结构单元)to duplicate cellular content.
Therefore, glucose is redirected towards the generation of one-carbon metabolites (methylenetetrahydrofolate (CH2-THF) and SAMe) and two-carbon (acetyl-CoA) units for lipid synthesis, the build-up of reducing power under the form of NADPH, the maintenance of the cellular redox state through the regeneration of NAD+ and the production of nucleotides through the PPP.
因此，葡萄糖被引导产生一碳代谢物(亚甲基四氢叶酸(CH2-THF)和二碳(乙酰辅酶 A)单元用于脂质合成，NADPH 形式的还原力的建立，通过 NAD+的再生维持细胞的氧化还原状态，以及通过 PPP 产生核苷酸。
Most of these adaptations depend on the ability of cells to convert pyruvate into lactate under aerobic conditions, both for the regeneration of NAD+ and for boosting the production of reductive power in the form of NADPH (termed the Warburg effect, turquoise arrows).
GSH, glutathione; GSSG, glutathione disulfide; SAH, S-adenosyl-l-homocysteine.
Here, glucose is catabolized through glycolysis, thus generating two molecules of ATP, NADH and acetyl-CoA. （efficient generation of ATP requires/needs more time?）
Both NADH and acetyl-CoA are then consumed in the mitochondria, generating an additional 34 molecules of ATP.
However, proliferating cells experience major anabolic needs for generation of biomolecules.
Specifically, one-carbon units and acetyl-CoA are directed to the synthesis of nucleotides and lipids, whereas the pentose-phosphate pathway (PPP) maintains RNA/ DNA and the reducing source NADPH, and lactate secretion maintains NAD+ regeneration and the redox balance.
This balancing of cellular demand and metabolite distribution is not limited to differences in division rates（maintenance[ˈmeɪntənəns] and proliferation is the two extremes）.
For example, neuronal, cardiac and hepatic lineage specifications all induce mitochondrial mass to sustain the elevated ATP requirements in these tissues.
Concordantly, the transcriptional networks responsible for either maintaining pluripotent stem cells or promoting differentiation directly induce glycolysis or mitochondrial biogenesis, respectively.
Therefore, the modulation of cellular metabolism is a cellular response for maintaining cellular pools of metabolites and thus sustaining cell-specific function.
● Metabolic pathways are highly compartmentalized ●
Because most of the metabolic network relies on the same metabolites, metabolic pathways must be compartmentalized to avoid futile cycles and to direct metabolite conversion towards the correct output.
futile[ˈfjuːtl] If you say that something is futile, you mean there is no point in doing it, usually because it has no chance of succeeding.
Metabolic enzymes have consequently become separated in time, space and subcellular location.
Fig. 2 | Metabolic fluxes are compartmentalized in time, space and subcellular organelles.
Because metabolic networks are highly interconnected, metabolic reactions are separated in time and space to avoid futile cycles and maximize output efficiency.
a, Metabolic output exhibits an oscillating profile.
Cell-cycle regulators such as cyclins and cyclin-dependent kinases modulate the metabolic network and sustain cell-stage-specific metabolic needs.
Whereas the preparation for S phase requires a metabolic reorientation of glycolysis towards nucleotide and NADPH production, the energy-demanding cell separation of M phase requires large amounts of energy and fragmentation of mitochondria for proper distribution.(random，even)
Second, feed-forward and feedback loops further control metabolic fluxes.
thus maintaining metabolite pools at optimal conditions.
Finally, the molecular components (of the oscillating circadian clock)feed into the regulation of cellular metabolism and anticipate metabolic demand (linked to fasting/feeding and sleep/exercise cycles. )
b, Metabolic enzymes exhibit local complexes that optimize pathway efficiency and specialize metabolic output in specific cellular subsites.
Migrating cells, such as sprouting endothelial cells, require high levels of ATP, specifically at the extending filopodia.
Therefore, enzymes involved in glycolysis form multienzyme complexes that are specifically sequestered(isolated) to the cytoskeleton at these local sites of cytoskeletal remodelling.
Formation of complexes both compartmentalizes pathways to specific cellular sublocations and diverts metabolic fluxes to a specific output through the increase in pathway efficiency.
Indeed, the different enzymes needed to generate purines are sequestered in a complex called the purisome located at the interface with mitochondria, thereby increasing the effectiveness of purine synthesis and providing access to mitochondrial formate甲酸.
PRPP, phosphoribosyl pyrophosphate; IMP, inosine 5′-monophosphate.
c, Metabolic pathways are separated through the subcellular localization of enzymes, thus diverting metabolic fluxes on the basis of local metabolite concentrations.
As part of one-carbon metabolism, serine provides the basis for various cytoplasmic biosynthetic reactions.
In the cytoplasm, serine is used for the production of proteins, haem, glutathione and phosphatidylserine. 在细胞质中，丝氨酸用于生产蛋白质、血红素、谷胱甘肽和磷脂丝氨酸。
Import of serine into the mitochondria diverts serine-derived carbon towards the mitochondrial arm of one-carbon metabolism; this flux is directed towards the formation of formate, the biosynthesis of nucleotides and the regeneration of homocysteine.
The requirement of much higher concentrations of NADP+ in mitochondria (to sustain the high demand for reducing power) is maintained through the one-carbon cycle running in opposite directions in the mitochondria versus the cytoplasm, thereby avoiding futile conversion.
PHGDH, phosphoglycerate dehydrogenase; MTR, methionine synthase; MTHFR, methylene tetrahydrofolate reductase; GLDC, glycine decarboxylase; CHO-THF, 10-formyl-THF.
● Temporal regulation through rhythmic activity and metabolic bursts ●
First, cell-cycle regulators proactively redirect metabolic fuels to anticipate changes in metabolic needs.
During G1 progression, D-type cyclins generate a fused mitochondrial structure through inhibition of the transcription factor NRF1 and the transcriptional coactivator PGC1α and block the pyruvate dehydrogenase complex in a manner dependent on the translation-initiation factor EF2A, thereby allowing for biomass production through the redistribution of glycolytic intermediates towards the PPP through modulation of phosphofructokinase and the pyruvate kinase PKM2.
在G1进程中，D型周期蛋白通过抑制转录因子NRF1和转录辅激活因子 pgc1α 而产生融合的线粒体结构，并以依赖翻译起始因子EF2A的方式阻断丙酮酸脱氢酶复合体，从而允许通过调节磷酸果糖激酶和丙酮酸 PKM2 而将糖酵解中间体重新分配到 PPP 而产生生物量(生物大分子)。
After the completion of S phase, Cdk1, Cdc25A and cyclin B redirect metabolism back towards energy production to sustain chromosomal segregation through the degradation of the GTPase MFN1, the promotion of the mitochondrial-protein-import channel TOM40 and the nuclear translocation of PKM2, coupled with subsequent induction of glycolytic enzymes.
The temporal activity of metabolic pathways is further fine-tuned through a system of feedback and feed-forward regulation.
Importantly, even in a constant environment, metabolic output relies on metabolic bursts rather than on continuous production.
Indeed, yeast cells that are kept in G0/G1 still exhibit a cycling profile, with short bursts of expression of genes that regulate oxygen consumption, autophagy and protein biosynthesis.
Feedback regulation of end metabolites to upstream enzymatic reactions is found at the transcriptional and activity levels, and has been observed in almost all biosynthetic processes, as particularly exemplified in pathways balancing amino acid, nucleotide and ATP levels (Fig. 2a).
Finally, circadian rhythms are another critical system that regulates the temporal expression of thousands of genes in anticipation of feeding/fasting and light/dark cycles, separating metabolic activity into 24-hour intervals.
The circadian clock is based on the activity of two core transcription factors, CLOCK and BMAL1, that activate a variety of gene programs and ultimately lead to an expression/feedback-inhibition cycle.
During feeding or energy expenditure, adipose tissue and skeletal muscle take up glucose, whereas fasting modulates glucose metabolism in the liver, thereby sustaining whole-body homeostasis.
As previously reviewed, almost all metabolic enzymes in the liver, skeletal muscle and adipose tissue, including those regulating gluconeogeneis, as well as glycogen, lipid and energy metabolism, are controlled by circadian rhythms.
This network responds to feeding and light cues, and consequently allows for the coordinated regulation of metabolites and metabolic enzymes (CircadiOmics42).
For instance, in skeletal muscle, the clock components align glycolysis and mitochondrial activity through both the regulation of hypoxia-inducible factor (HIF) signaling and the induction of mitochondrial fission by phosphorylation of DPR1, a dynamin superfamily GTPase.
In turn, metabolism also influences the clock machinery via fine-tuning of rhythms by the energy and nutrient sensors AMPK and mTOR, which destabilize and boost translation of clock components, respectively.
● Spatial separation through formation of enzyme complexes ●
Beyond their temporal separation, metabolic pathways are restricted to subcellular locations.
Especially for glycolytic enzymes, the formation of enzyme complexes, called metabolons, greatly increases hyperlocal energy production.
For example, glycolytic multienzyme complexes sequestered to the cytoskeleton generate high amounts of local ATP, which is used in the reorganization of cytoskeletal actin filaments during endothelial tip cell formation.
The formation of multienzyme complexes provides the dual advantage of localizing production and greatly increasing flux efficiency within the pathway encompassing（including） these enzymes, as illustrated by the formation of a purine biosynthesis complex (purisome).
Extensive studies, mainly performed in plant and bacterial systems, have identified dozens of multiprotein structures that perform metabolic functions, such as polyamine biosynthesis, proline catabolism and β-oxidation (Fig. 2b).
● Subcellular organelles physically separate metabolite pools ●
The most extreme form of metabolic compartmentalization is accomplished through the physical separation of metabolite pools at organelle structures, each functioning as an independent metabolic subunit (Fig. 2c).
The clearest example of this compartmentalization is that of the mitochondrion: this separate entity within the cell isolates metabolites and metabolic enzymes from the cytoplasm, thus allowing for a specific group of reactions to occur only within the organelle.
Controlled intake and secretion of metabolites such as pyruvate, serine, glutamine, SAMe and NAD+ are regulated by a set of specific transporters collectively termed the mitochondrial carriers.
The importance of physically separating metabolite pools is clearly illustrated in the diverse roles of NAD+ metabolism.
In the cytoplasm and nucleus, NAD+ is an important cofactor for poly(ADP–ribose) polymerases (PARPs), sirtuins and enzymes involved in biosynthesis.
Because the levels of NAD+ in these locations hover around the Michaelis constant of these enzymes, the nuclear pathways involved in DNA repair, metabolic reprogramming and biosynthesis are balanced by NAD+ availability.
由于这些位置的NAD+水平徘徊在这些酶的米切里斯常数附近，参与DNA修复、代谢重编程和生物合成的核通路被NAD+的可用性所平衡。
However, in the mitochondrial compartment, NAD+ acts as a transfer molecule linking oxidative phosphorylation to ATP production and is therefore found in much higher concentrations than those in the cytoplasm.
The mitochondrial membrane separates one-carbon pools.
The mechanisms controlling metabolite compartmentalization have been identified mostly with regards to the interconnected activity of folate（叶酸） and methionine cycle.
In this cycle (one-carbon metabolism), carbon units derived from methionine, serine and glycine are transferred to reactive intermediates for use in nucleotide and polyamine production or as a substrate for a variety of methyltransferases.
Remarkably, the folate cycle consists of reversible reactions that represent a mirror image in the cytoplasmic versus mitochondrial compartments, each controlled by organelle-specific isoforms.
One-carbon units from serine are reversibly transferred to the carbon carrier tetrahydrofolate (THF) by serine hydroxymethyl transferase (SHMT1 in the cytoplasm and SHMT2 in mitochondria).
Then 5,10-methylenetetrahydrofolate can be further metabolized first to 10-formyl-THF and finally to formate through the activity of methylenetetrahydrofolate dehydrogenase (MTHFD1 in the cytoplasm, or MTHFD2 and MTHFD2L in the mitochondria;
然后，5,10-亚甲基四氢叶酸可以进一步先代谢为10-甲酰基- THF，最后（通过亚甲基四氢叶酸脱氢酶(细胞质中的MTHFD1，线粒体中的MTHFD2和MTHFD2L)的活性）形成甲酸；
Because one-carbon units can be transported between the cytoplasm and nucleus only in the forms of serine, glycine and formate, this compartmentalization offers an opportunity to steer one-carbon units towards specific pools.
Mitochondrial serine import regulates one-carbon-metabolism activity.
In proliferating cells, one-carbon units are derived mainly from mitochondrial serine catabolism, thus ultimately leading to the generation of formate, which can be transported back to the cytoplasm for either nucleotide biosynthesis or reconversion to serine64,65 (Fig. 2c).
Genetic disruption of mitochondrial serine catabolism leads to a cytoplasmic formate deficit and a reversal of the activity of the cytoplasmic isoforms, leading to nucleotide biosynthesis without any metabolite transfer into the mitochondria.
However, this perturbation dysregulates the distribution of serine towards its different metabolic consumers and leads to an inability to generate sufficient amounts of serine through de novo biosynthesis.
Given that de novo serine biosynthesis is an exclusively cytoplasmic reaction important in a variety of metabolic reactions，serine import provides a way to distribute serine to either cytoplasmic reactions or mitochondrial one-carbon metabolism (Fig. 2c).
These studies identify the mitochondrial serine transporter as a gatekeeper that regulates the balance of serine availability in both compartments.
Physical separation generates distinct metabolic environments.
In addition to regulating influx and efflux, metabolic compartmentalization allows reactions to occur in specific metabolic environments.
For instance, the factor driving one-carbon directionality relies on the local ratio of NADP+ to NADPH.
Whereas the reduction of NAD+ to NADH captures the electrons that drive ATP synthesis, the conversion of NADP+ to NADPH stores the reducing power needed for biosynthetic reactions.
NADP+ can be converted from and into NAD+ and although a recent study has indicated that de novo synthesis of NADP via a NAD kinase may be important in cells with activated protein kinase B (AKT), the balance between NADP+ and NADPH is determined primarily through the activity of cytoplasmic and mitochondria-specific pathways.
Lewis and colleagues have traced mitochondrial NAPDH to the activity of MTHFD2，whereas the much higher cytoplasmic levels are sustained by the oxidative branch of the PPP.
Therefore, the concentrations of NADP+ and NADPH in the cytoplasmic and mitochondrial compartments regulate the activity of MTHFD1 and MTHFD2 and correctly direct one-carbon flux.
This directionality in turn is important for replenishing the methylation cycle.
In the cytoplasmic methionine cycle, the universal methyl donor SAMe is generated through the catalytic linking of ATP and methionine through the activity of the methionine adenosyltransferase MAT2A.
When methionine is not available, SAMe can also be regenerated through the folate-cycle-dependent methylation of homocysteine.
This process occurs in the cytoplasm, where the methyl donor used for methylation of homocysteine is generated rather than consumed by MTHFD1.
These insights clearly show that cellular metabolism is aimed not only at maintaining the pools of key metabolites but also at redirecting metabolite pools among compartments with different needs.
As explained in detail in recent reviews，the same concepts of compartmentalization apply to acetyl and acyl moieties.
In addition, mitochondrial transporters for pyruvate, succinate and propionate, and enzymes modulating acetate and crotonate levels, regulate the exchange of metabolite pools between the mitochondrial and cytoplasmic compartments, thus maintaining a homeostatic balance in these separate metabolic environments.
● Chromatin as a linchpin connecting metabolism to epigenetic regulation ●
Because the cellular location of a metabolic reaction matters, the nucleus has been postulated to exhibit compartmentalization of metabolic activity.
Given the large size of nuclear pores3 , metabolites are believed to freely diffuse between the nucleus and the cytoplasm.
Yet, the nucleus is characterized by a set of specific metabolic requirements that link metabolism to cellular fate.
Fig. 3 | The nucleus is an underappreciated but separated metabolic compartment.
a, Chromatin dynamics in the nucleus is intertwined（cross link） with cellular metabolism, because metabolites constitute main histone and DNA modifications, whereas the activity of numerous chromatin modifiers relies on the presence of specific nuclear metabolites as cofactors.
Details are provided in the main text. GlcNAc, N-acetylglucosamine; HAT, histone acetyltransferase; HMT, histone methyltransferase; SIRT; sirtuin; KDM, lysine demethylase; 3PG, 3-phosphoglyceric acid; IDH/SDH/FH, isocitrate dehydrogenase/succinate dehydrogenase/fumarate hydratase; 2-HG, 2-hydroxyglutarate; Ac, acetyl; Me, methyl; X, other modifications, including lactylation, phosphorylation and GlcNacylation.
b, Concentrations of nuclear metabolites are not merely dependent on diffusion from the cytoplasm but can be actively exchanged between the nuclear and non-nuclear compartments to sustain cellular homeostasis.
Overproduction of acetyl and methyl groups increases histone acetylation and histone and DNA methylation, respectively, thus making chromatin as an important metabolite sink.
This fixed storage of metabolites can then be mobilized to sustain cellular metabolism according to need. Regulation of nuclear metabolism is accomplished through the availability of nuclear metabolites, the activity of chromatin modifiers, and the active import and export of nuclear metabolic enzymes.
For example, PARP-1 activity can be shut down by decreasing nuclear NAD+ through the downregulation of NMNAT1. The two mechanisms controlling the exchange in metabolites in and from the nucleus consist of the modulation of chromatin modifiers to either increase or decrease metabolite retention on chromatin, or the activity of the nuclear pore complex (NPC), which imports or exports nucleus-oriented metabolic enzymes.
HDAC, histone deacetylase; NAM, nicotinamide.
● Metabolism epigenetically determines cellular fate ●
Evidence of a link between nuclear metabolism and cell fate has grown in recent years.
Even the modulation of a few metabolites is sufficient to drive cell-fate changes.
For example, the treatment of pluripotent stem cells with palmitic(棕榈酸) acid drives neural lineage specification through the production of eicosanoid signalling molecules.
Similarly, elevated extracellular amino acid levels induce hepatocyte differentiation through both the modulation of mitochondrial metabolism and the induction of a hepatic transcriptional network aimed at catabolizing extracellular amino acids.
Although how metabolites affect fate remained unclear for years, emerging studies indicate a major role of chromatin dynamics.
Chromatin marks are chemical modifications on histones or DNA that determine DNA accessibility, transcription-machinery recruitment and chromatin condensation.
The most extensively studied chromatin modifications are methylation of DNA and acetylation/ methylation of histones.
In general, DNA methylation is associated with both inhibition of transcription and chromatin compaction, whereas acetylation of the lysine residues of histones is associated with activation of transcription.
Histone methylation can either promote or repress transcription depending on the specific lysine residue modified.
Furthermore, a growing list of novel chromatin modifications, such as histone phosphorylation, acylation or conjugation to O-linked β-N-acetylglucosamine (O-GlcNAC), have all been found to influence transcription.
Importantly, the activity of the chromatin modifiers that add or remove these marks critically depends on a few metabolites, thus linking metabolism and epigenetic modifications.
For instance, the intracellular levels of α-ketoglutarate (αKG) have been found to control the expression of hundreds of genes.
Elevation of αKG is sufficient to mimic the phenotype of the entire p53 antitumour/differentiation response; it also greatly improves reprogramming efficiency, maintains naive pluripotent stem cells, and accelerates the differentiation of primed pluripotent stem cells, colon cancer cells and epidermal stem cells.
αKG exerts its function as a coactivator of histone demethylases and TET demethylases, which remove methylation marks from chromatin.
Therefore, whereas the maintenance of global hypomethylation supports stemness in hypomethylated naive stem cells, the activation of differentiation genes through the removal of closed-chromatin methylation marks explains the prodifferentiation effect of αKG in the latter models.
● Metabolite levels dictate chromatin modifications ●
The dependency of chromatin modifiers on metabolites for driving the chemical conversion of histones and DNA indicates a direct link between metabolism and epigenetics.
Indeed, the universal one- and two-carbon donors SAMe and acetyl-CoA are the essential substrates required for the methylation and acetylation of chromatin, whereas histone phosphorylation, acylation or O-GlcNACylation are dependent on the incorporation of ATP, acyl moieties and O-GlcNAC, respectively.
As a result, increasing or decreasing the pools of these 'epigenetic metabolites’ directly affects the epigenome.
For instance, animal studies have found that restriction of the SAMe precursor methionine significantly affects levels of SAMe as well as methylation patterns of DNA and histones.
Specifically in cancer, methionine restriction decreases trimethylated histone H3 lysine 4 (H3K4me3), thus resulting in downregulation of cancer-associated genes such as AKT1, MYC and MAPK.
Furthermore, deposition of the H3K4me3 or H3K36me3 histone marks on genes regulating activation of helper T cells and macrophages, respectively, are fuelled through the upregulation of methionine-dependent SAMe production.
Changes in acetyl-CoA levels have also been shown to directly affect histone acetylation levels.
The rate of acetyl-CoA synthesis through glycolysis directly correlates with the levels of approximately half of all histone acetylation sites.
Furthermore, high levels of acetate not only contribute carbons to lipid synthesis but also activate the expression of genes involved in lipid synthesis, through increased acetylation of H3K9, H3K27 and H3K56 in lipid-synthesis-associated genes. (Methylation of DNA and histone is mutually exclusive with histone acetylation )
In accordance, cellular acetyl-CoA levels in yeast directly determine the acetylation states of histones in the promoters of proliferation-associated genes, thus linking cellular fitness with growth rates.
The influence of metabolites on cell fate is further exemplified by the recent discovery that lactate, such as that present in the hypoxic tumour microenvironment or in sepsis（damaged tissue； the presence of pus-forming bacteria in the body）, can remodel macrophage[ˈmækrəfeɪdʒ behaviour through generating a previously unknown histone modification, histone lactylation.
● Nuclear metabolism allows for local control of chromatin dynamics ●
The studies described above indicate that the epigenome is influenced by metabolite availability.
Yet, the maintenance of epigenetic marks is vital to sustaining cellular identity.
Therefore, molecular systems might exist to isolate the nuclear compartment and to shield the epigenome from the putative [ˈpjuːtətɪv] detrimental metabolic fluctuations that occur under physiological conditions.
Because no physical barrier is present to regulate nuclear metabolite levels，two additional mechanisms specify metabolic conversions in the nucleus and distribute metabolites between the nuclear and cytoplasmic compartments.
These systems involve the retention of metabolites on chromatin and/or the local production and consumption of metabolites by nuclear complexes.
● Chromatin acts as a reservoir of methyl and acetyl groups ●
reservoir/ˈrɛzəˌvwɑː/ A reservoir is a lake that is used for storing water before it is supplied to people.
Chromatin has recently been identified as a reservoir for metabolites that can store a metabolite surplus[ˈsɜːrplʌs] or supplement cellular pools in times of need (Fig. 3b).
Although changes in the epigenome can have widespread consequences on cellular functions, the global epigenetic modifications of histones appear to be sufficiently robust to not rely on single methylation or acetylation marks, thus allowing for some level of metabolite storage and exchange.
Chromatin modifiers can establish 'methylation reservoirs’.
The activation or silencing of specific loci is influenced by a combination of epigenetic marks on histones in promoter and enhancer sequences, the gene body, and facultative and constitutive heterochromatin.
兼性异染色质(facultative heterochromatin)：
在一定时期的特种细胞的细胞核内, 原来的常染色质可转变成兼性异染色质。如雄性个体的细胞含有一个瘦小的Y染色体和一个大的X染色体, 由于X和Y染色体上很少有共同的基因, 对于雄性来说, X染色体上的基因就只有一个拷贝。
虽然雌性细胞有两条X染色体, 也只有一条具有转录活性, 另外一条X染色体像异染色质一样保持凝缩状态, 称为巴氏小体(Barr bady)。
巴氏小体的形成保证了雄性和雌性都只有一条具有活性的X染色体, 合成等量的X-连锁基因编码的产物。
A combinatory code consequently could buffer the effects of small fluctuations in methylation or acetylation on transcription and cell identity.
Studies have shown that 30% of CpG islands are free of methylation, whereas almost half of yeast histones lack acetylation at any given time.
Therefore, as two independent studies have calculated, the total storage capacity of the epigenome for methyl groups is more than 1,000 times larger than the total cellular SAMe pool, and large stretches of methylated chromatin have been postulated to encompass metabolic sinks or stores for methyl groups.
In yeast, scientists have shown that specifically methylated H3K36 and H3K79 retain methyl groups after SAMe accumulation, whereas in parallel, these moieties can be mobilized to sustain the cytoplasmic generation of phospholipids after SAMe depletion..
Methylation of H3K36 is found throughout gene bodies and has been implicated in transcriptional elongation and termination, or defining exon sequences.
Furthermore, although methylated H3K79 was initially identified to mediate telomeric silencing, this methyl mark was later observed to occupy almost 90% of all yeast histones and to shunt silencing factors towards silenced loci.
Additionally, H3K79 methylation has been linked to transcriptional elongation, because it is present in active gene bodies.
H3K36 and H3K79 could function as an efficient nuclear reservoir or store for methyl groups if small fluctuations only marginally affect transcription and cell fate.
Fig. 4 | Regulatory mechanisms balance metabolites between the nuclear and non-nuclear compartments.
a, After overproduction of SAMe, the activity of both nuclear methyltransferases (MTs) and genes involved in proliferation increases, whereas SAMe production is inhibited, and methyl groups are stored on chromatin.
Concordantly, a shortage of SAMe shuts down proliferation and mobilizes methyl groups from heterochromatin, thereby releasing formate and maintaining cellular homeostasis.
TCA, tricarboxylic acid cycle.
b, After overproduction of acetyl-CoA, histone acetylation induces proliferation and the storage of acetyl-CoA in the form of fat.
Acetylation of H4K8 and H4K16 might provide a nuclear store.
Nuclear production and recycling of acetyl-CoA appear to be regulated through the import of metabolic enzymes into the nucleus, and the histone deacetylase SIRT6 might have evolved to modulate glycolysis and fat storage in response fatty acids, which in turn depend on acetyl-CoA levels.
The circadian-clock components also influence histone acetylation, mainly through regulating the levels of SIRT1.
FASN, fatty acid synthase; ACOX1, acyl-CoA oxidase 1; PDC, pyruvate dehydrogenase complex.
c, The regeneration of NAD+ is accomplished through the activity of a nuclear, cytoplasmic or mitochondrial isoform of NMNAT and through the selective import of NAMPT into the nucleus. Given the much higher concentration of NAD+ in the mitochondrial compartment, mitochondrial NAD+ or NMN might serve as the cellular reservoir.
In addition, the clock components induce an oscillating NAD+ profile through rhythmic regulation of NAMPT expression.
OXPHOS, oxidative phosphorylation.
Indeed, the initial study in yeast did not find a correlation between demethylation of H3K36 and H3K79 and transcriptional changes.
In addition, a recent study has indicated that after methionine restriction, mammalian cells mobilize methyl groups specifically from H3K9me3 and H3K9me2, both of which are located in highly methylated constitutive and facultative heterochromatin, while protecting the H3K9me1 mark, thereby maintaining silencing and minimally affecting cell fate(Fig. 4a).
Major fluctuations in the methylation density on histones and DNA can induce a loss of cell identity，aberrant expression and genomic instability.
Controlled release and retention of marks, even those linked to methylation reservoirs or stores, remain extremely important. Inhibition of H3K36 methyltransferases blocks mesenchymal progenitor differentiation and induces undifferentiated sarcomas, possibly through its intergenic role in antagonizing H3K27me3 propagation.
Furthermore, methylation defects at H3K79 are pathogenic, because overdeposition through disrupted localization of the H3K79 methyltransferase DOT1L induces mixed-lineage leukaemia, whereas DOT1 deletion is embryonic lethal.
Although constitutive heterochromatin might be considered a large methylation reservoir, its flexibility is limited. Overdepletion of H3K9 methylation as a result of dysfunction of the Suv39h histone methyltransferase results in demethylation of large stretches of pericentric heterochromatin accompanied by chromosomal instability.
Furthermore, high levels of demethylation of heterochromatic histones and DNA induce the reactivation of satellite repeats and LINE1 retrotransposons, both of which are linked to cellular dysfunction and carcinogenesis126. Likewise, inhibition of histone demethylase activity results in hypermethylation of H3K9, thus impairing homologous-recombination-based repair of double-strand breaks (DSBs)123.
These studies identify nuclear methyl reservoirs as marks that are highly abundant in chromatin, such that a relatively small methyl depletion or increase does not affect transcription.
In addition, because epigenetic methyltransferases exhibit a wide range of Michaelis–Menten kinetics, uncharacterized systems might be in place to preferentially mobilize or deposit SAMe on H3K36, H3K79 and H3K9me2/me3 after depletion or overproduction of the metabolite127.
Because most studies have focused on bulk changes in methylation, future studies should determine whether these systems can target specific regions, such as gene bodies, facultative and constitutive heterochromatin, or telomeric regions, for methyl mobilization or storage.
Fig. 5 | The formation of complexes on chromatin, including metabolic enzymes, drives hyperlocal metabolic conversions.
In the nucleus, as in other compartments, metabolic enzymes form multienzyme complexes that increase the efficiency of hyperlocal metabolic flux and guide metabolic conversion towards certain chromatin modifications In yeast, a large complex has been isolated that links enzymes responsible for glycolysis, and for serine and SAMe biosynthesis, to the histone methyltransferase SET1 and the histone phosphorylase PYK1, providing all components to sustain epigenetic methylation and phosphorylation. Similarly, in mammals, the α-KGDH complex can fuel the histone acyltransferase KAT2A, which in turn drives H3K79 succinylation through the formation of multienzyme complexes. Finally, the activity of histone acetyl transferases and of the NAD+ consuming PARP1 enzyme is sustained through local recycling of nuclear acetyl-CoA (by ACSS2) and NAD+ moieties (by NMNAT1), respectively. Studies indicate that the activity of chromatin modifiers appears to be dependent on the expression and activity of nuclear metabolic enzymes rather than on the exchange in metabolites between the cytoplasm and nucleus. PEP, phosphoenolpyruvate.
