Microbial Regulation of Host Physiology by Short-chain Fatty Acids

Short chain fatty acids (SCFAs) contribute to intestinal homeostasis and the regulation of energy metabolism.SCFAs circulating in the blood influence tissue-specific acetylation of histones 3 and 4 in a tissue-specific fashion.Delivery of SCFAs to the colon, using specialized diets, prevents onset of diabetes in nonobese diabetic (NOD) mice.During gestation, SCFAs can cause epigenetic imprinting in utero and protect against allergic airway disease.SCFAs regulate the blood–brain barrier and neuroimmunoendocrine functions. Our ancestral diet consisted of much more nondigestible fiber than that of many societies today. Thus, from an evolutionary perspective the human genome and its physiological and nutritional requirements are not well aligned to modern dietary habits. Fiber reaching the colon is anaerobically fermented by the gut bacteria, which produce short-chain fatty acids (SCFAs) as metabolic by-products. SCFAs play a role in intestinal homeostasis, helping to explain why changes in the microbiota can contribute to the pathophysiology of human diseases. Recent research has shown that SCFAs can also have effects on tissues and organs beyond the gut, through their circulation in the blood. SCFAs not only signal through binding to cognate G-protein-coupled receptors on endocrine and immune cells in the body but also induce epigenetic changes in the genome through effects on the activity of histone acetylase and histone deacetylase enzymes. Furthermore, epigenetic imprinting likely occurs in utero, highlighting the importance of the maternal diet in early life. Here we review current understanding of how SCFAs impact on human and animal physiology and discuss the potential applications of SCFAs in the prevention and treatment of human diseases. Our ancestral diet consisted of much more nondigestible fiber than that of many societies today. Thus, from an evolutionary perspective the human genome and its physiological and nutritional requirements are not well aligned to modern dietary habits. Fiber reaching the colon is anaerobically fermented by the gut bacteria, which produce short-chain fatty acids (SCFAs) as metabolic by-products. SCFAs play a role in intestinal homeostasis, helping to explain why changes in the microbiota can contribute to the pathophysiology of human diseases. Recent research has shown that SCFAs can also have effects on tissues and organs beyond the gut, through their circulation in the blood. SCFAs not only signal through binding to cognate G-protein-coupled receptors on endocrine and immune cells in the body but also induce epigenetic changes in the genome through effects on the activity of histone acetylase and histone deacetylase enzymes. Furthermore, epigenetic imprinting likely occurs in utero, highlighting the importance of the maternal diet in early life. Here we review current understanding of how SCFAs impact on human and animal physiology and discuss the potential applications of SCFAs in the prevention and treatment of human diseases. SCFAs have fewer than six carbons in the aliphatic tail, and the most abundant in the intestine are acetate (C2), propionate (C3), and butyrate (C4). SCFAs are a metabolic by-product of microbial fermentation of complex polysaccharides not digested, or only partly digested, in the human small intestine. These nondigestible polysaccharides (NDPs) are found in plant cell walls and are further classified into soluble and nonsoluble dietary fibers. The soluble NDPs are highly fermentable and typically generate greater quantities of SCFAs in the colon than do soluble fibers. Currently there are three well characterized human SCFA-sensing G-protein-coupled receptors (GPCRs) which are differentially expressed on different sets of immune cells as well as epithelium and endocrine cells central to the regulation of metabolism (Table 1). Studies in GPCR-gene-deficient mice have established the importance of SCFA signaling through these metabolite receptors in the control of inflammation and intestinal homeostasis but the functional roles of these receptors on different cell types is still not fully understood.Table 1Summary of Currently Recognized SCFA-binding GPCRs, Their Ligands, Associated G-protein-effector Mechanisms, and Likely Expression in Different Cell TypesaAbbreviations: DC, dendritic cells; mdDC, monocyte-derived DC.ReceptorAlternativeCarbonsFatty acidTransductionTissueCell typeRefsGPCR41FFAR3C2-C5Acetate, propionate, butyrate, formateGi/o, β-gastductinIntestine, adipose tissue, spleen, immune cells, pancreasEnteroendocrine L-cells, monocytes, neutrophils, mdDC, adipocytes,[1.Brown A.J. et al.The orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids.J. Biol. Chem. 2003; 278: 11312-11319Abstract Full Text Full Text PDF PubMed Scopus (1381) Google Scholar]GPCR43FFAR2C2-C5Acetate, propionate, butyrate, formate, pentanoateGi/o, Gq, β-arrestin-2Intestine, adipose tissue, skeletal muscle, immune cells, spleen, pancreasEnteroendocrine L-cells, beta-cells, adipocytes, B/T-cells, myeloid cells, monocytes[2.Thangaraju M. et al.GPR109A is a G-protein-coupled receptor for the bacterial fermentation product butyrate and functions as a tumor suppressor in colon.Cancer Res. 2009; 69: 2826-2832Crossref PubMed Scopus (369) Google Scholar,3.Zhao Y. et al.GPR43 mediates microbiota metabolite SCFA regulation of antimicrobial peptide expression in intestinal epithelial cells via activation of mTOR and STAT3.Mucosal Immunol. 2018; 11: 752-762Crossref PubMed Scopus (134) Google Scholar]GPCR109AHCAR2, NIACR1C4Butyrate, niacinGi/o, β-arrestin-1Immune cells, intestine (lumen), adipose tissueDendritic cells, macrophages, epithelial cells, mdDC, DC, macrophages, monocytes[2.Thangaraju M. et al.GPR109A is a G-protein-coupled receptor for the bacterial fermentation product butyrate and functions as a tumor suppressor in colon.Cancer Res. 2009; 69: 2826-2832Crossref PubMed Scopus (369) Google Scholar,3.Zhao Y. et al.GPR43 mediates microbiota metabolite SCFA regulation of antimicrobial peptide expression in intestinal epithelial cells via activation of mTOR and STAT3.Mucosal Immunol. 2018; 11: 752-762Crossref PubMed Scopus (134) Google Scholar]OLFR78 (m), OR51E2 (h)PSGRC2-C3Acetate, propionateGαs, unknownProstate, colon, lungEnteroendocrine cells, prostate epithelium, airway smooth muscle cells, melanocytes[4.Pluznick J.L. et al.Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation.Proc. Natl. Acad. Sci. U. S. A. 2013; 110: 4410-4415Crossref PubMed Scopus (564) Google Scholar, 5.Fleischer J. et al.Expression of odorant receptor Olfr78 in enteroendocrine cells of the colon.Cell Tissue Res. 2015; 361: 697-710Crossref PubMed Scopus (48) Google Scholar, 6.Aisenberg W.H. et al.Defining an olfactory receptor function in airway smooth muscle cells.Sci. Rep. 2016; 638231Crossref PubMed Scopus (54) Google Scholar]a Abbreviations: DC, dendritic cells; mdDC, monocyte-derived DC. Open table in a new tab Over the past century fiber intake by humans has decreased substantially as compared to the communities of populations eating traditional high-fiber diets [7.Sonnenburg E.D. Sonnenburg J.L. The ancestral and industrialized gut microbiota and implications for human health.Nat. Rev. Microbiol. 2019; 17: 383-390Crossref PubMed Scopus (104) Google Scholar]. This is especially the case in high-income countries where allergy, type 1 diabetes, inflammatory bowel disease (IBD), and autoimmune diseases have steadily increased over the past 60 years [8.Thorburn A.N. et al.Diet, metabolites, and 'western-lifestyle' inflammatory diseases.Immunity. 2014; 40: 833-842Abstract Full Text Full Text PDF PubMed Scopus (500) Google Scholar]. The importance of nondigestible fiber to health has recently been highlighted by a systematic review and meta-analyses of prospective studies and randomized controlled trials [9.Reynolds A. et al.Carbohydrate quality and human health: a series of systematic reviews and meta-analyses.Lancet. 2019; 393: 434-445Abstract Full Text Full Text PDF PubMed Scopus (396) Google Scholar]. The results suggest a 15–30% decrease in all causes of cardiovascular-related mortality, type 2 diabetes, and colorectal cancer when comparing high- and low-fiber consumers [9.Reynolds A. et al.Carbohydrate quality and human health: a series of systematic reviews and meta-analyses.Lancet. 2019; 393: 434-445Abstract Full Text Full Text PDF PubMed Scopus (396) Google Scholar]. SCFAs are now taking center stage as key players in the interactions with the host that impact on health and disease, especially given recent evidence for their capacity to modify the epigenome and effects on tissues and organs beyond the gut. Here we review the proposed mechanisms by which specific SCFAs may impact on host physiology and the in vivo evidence for their health benefits. Finally, we highlight the major findings and outstanding questions which will help to exploit SCFAs for the prevention and treatment of human diseases. Early studies in human cases of sudden death showed that SCFAs are produced in high amounts by the gut microbiota, reaching concentrations of around 13 ± 6 mmol/kg content in the terminal ileum and 80 ± 11 mmol/kg content in the descending colon [10.Cummings J.H. et al.Short chain fatty acids in human large intestine, portal, hepatic and venous blood.Gut. 1987; 28: 1221-1227Crossref PubMed Scopus (1689) Google Scholar]. In all parts of the colon acetate is at least twofold higher in concentration than propionate or butyrate. Measurements of acetate, propionate, and butyrate in the ascending colon, where most saccharolytic fermentation occurs, varies depending on the geographic origin of the cohort, but acetate typically accounts for about 60–75% of the total fecal SCFAs [11.Parada Venegas D. et al.Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases.Front. Immunol. 2019; 10: 277Crossref PubMed Scopus (580) Google Scholar]. Nutritionally specialized bacteria in the phyla Firmicutes and Actinobacteria are considered to be important in initiating the degradation of NDPs [12.Louis P. Flint H.J. Formation of propionate and butyrate by the human colonic microbiota.Environ. Microbiol. 2017; 19: 29-41Crossref PubMed Scopus (647) Google Scholar]. The continued breakdown of complex carbohydrates is attributed to certain abundant species within the phylum Bacteroidetes (Figure 1). Acetate production is common to many bacterial groups in the phylum Bacteroidetes, one of the largest groups in the intestine [10.Cummings J.H. et al.Short chain fatty acids in human large intestine, portal, hepatic and venous blood.Gut. 1987; 28: 1221-1227Crossref PubMed Scopus (1689) Google Scholar]. Propionate is produced by a few dominant genera, including the cornerstone species Akkermansia muciniphila [13.Derrien M. et al.Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.Int. J. Syst. Evol. Microbiol. 2004; 54: 1469-1476Crossref PubMed Scopus (945) Google Scholar]. Bacteroides vulgatus and Bacteroides thetaiotaomicron are also producers of propionate through the succinate pathway [14.Frost G. et al.The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism.Nat. Commun. 2014; 5: 3611Crossref PubMed Scopus (672) Google Scholar]. Coprococcus catus has been reported to consume lactate and utilize the acrylate pathway for propionate production [14.Frost G. et al.The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism.Nat. Commun. 2014; 5: 3611Crossref PubMed Scopus (672) Google Scholar]. Butyrate can be synthesized through four different pathways: acetyl-CoA, glutamate, lysine, and succinate [12.Louis P. Flint H.J. Formation of propionate and butyrate by the human colonic microbiota.Environ. Microbiol. 2017; 19: 29-41Crossref PubMed Scopus (647) Google Scholar]. Butyrate is produced by clostridial clusters I, III, IV, XI, XIVa, XV, and XVI of obligate anaerobes, of which cluster XIVa and cluster IV bacteria, related to Faecalibacterium prausnitzii, are the most abundant groups in humans. Members of clostridial cluster IX are also propionate producers via the lactate pathway. Small amounts of other SCFAs are also produced in the gut, namely caproate, formate, and valerate. Valerate can be formed by elongation of propionate in the presence of methanol as an electron donor [15.de Smit S.M. et al.Continuous n-valerate formation from propionate and methanol in an anaerobic chain elongation open-culture bioreactor.Biotechnol. Biofuels. 2019; 12: 132Crossref PubMed Scopus (20) Google Scholar]. Caproate can be formed by butyrate or acetate, or directly from lactate as an electron donor [16.Zhu X. et al.Production of high-concentration n-caproic acid from lactate through fermentation using a newly isolated Ruminococcaceae bacterium CPB6.Biotechnol. Biofuels. 2017; 10: 102Crossref PubMed Scopus (96) Google Scholar]. However, there are metabolic links between different types of bacteria, for example acetate produced by Bacteroidetes species can be utilized by species of Firmicutes to produce butyrate. SCFAs can be passively taken up by epithelial cells but in greater amounts by active transport via the monocarboxylate transporter 1 (MCT-1) and to a lesser extent the sodium-coupled monocarboxylate transporter 1 (SMCT-1) [17.Halestrap A.P. Meredith D. The SLC16 gene family-from monocarboxylate transporters (MCTs) to aromatic amino acid transporters and beyond.Pflugers Arch. 2004; 447: 619-628Crossref PubMed Scopus (768) Google Scholar,18.Sepponen K. et al.Expression of CD147 and monocarboxylate transporters MCT1, MCT2 and MCT4 in porcine small intestine and colon.Vet. J. 2007; 174: 122-128Crossref PubMed Scopus (21) Google Scholar]. SCFAs, especially butyrate, can be metabolized by colonocytes, providing 60–70% of their energy supply [19.Clausen M.R. Mortensen P.B. Kinetic studies on colonocyte metabolism of short chain fatty acids and glucose in ulcerative colitis.Gut. 1995; 37: 684-689Crossref PubMed Scopus (128) Google Scholar]. The remaining SCFAs are transported out of the cell across the basolateral membrane via an unknown HCO3− exchanger, suggested to be monocarboxylate transporter (MCT) 4 or 5 [20.den Besten G. et al.The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism.J. Lipid Res. 2013; 54: 2325-2340Abstract Full Text Full Text PDF PubMed Scopus (1938) Google Scholar]. In the mucosa, SCFAs can enter the blood capillaries and reach the liver via the portal vein. The liver clears a major part of propionate and butyrate from the portal circulation, but acetate can reach 200 μM in the venous serum of humans and pigs [18.Sepponen K. et al.Expression of CD147 and monocarboxylate transporters MCT1, MCT2 and MCT4 in porcine small intestine and colon.Vet. J. 2007; 174: 122-128Crossref PubMed Scopus (21) Google Scholar,21.Bloemen J.G. et al.Short chain fatty acids exchange across the gut and liver in humans measured at surgery.Clin. Nutr. 2009; 28: 657-661Abstract Full Text Full Text PDF PubMed Scopus (177) Google Scholar]. The rapid absorption of SCFAs, and their metabolism by intestinal epithelium and liver, means that they can make a substantial contribution to the caloric requirements of humans and other animals. In herbivorous ruminants, about 70% of the caloric requirement comes from SCFAs, and about 10% in omnivorous humans and pigs [23.Bergman E.N. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species.Physiol. Rev. 1990; 70: 567-590Crossref PubMed Scopus (1497) Google Scholar]. In patients with short-bowel syndrome (SBS), who lack a functional small intestine, NDPs have been used as a dietary strategy to overcome malabsorption because the SCFAs produced by bacterial fermentation in the colon can provide up to 1000 kcal per day [24.Nordgaard I. et al.Importance of colonic support for energy absorption as small-bowel failure proceeds.Am. J. Clin. Nutr. 1996; 64: 222-231Crossref PubMed Scopus (147) Google Scholar,25.Parrish C.R. DiBaise J.K. Managing the adult patient with short bowel syndrome.Gastroenterol. Hepatol. 2017; 13: 600-608PubMed Google Scholar]. SCFAs are also important for stimulating sodium and water absorption in the colon through the regulation of nutrient and ion transporters which can also help against diarrhea associated with SBS [26.Tappenden K.A. et al.Glucagon-like peptide-2 and short-chain fatty acids: a new twist to an old story.J. Nutr. 2003; 133: 3717-3720Crossref PubMed Scopus (68) Google Scholar]. Many common dietary metabolites are sensed by host GPCRs as a mechanism for the host to optimize responses and for survival with limiting nutrients (Figure 1 and Table 1). The same holds true for SCFAs which signal through three main GPCRs (Table 1). SCFA signaling through GPCRs on enteroendocrine cells, pancreatic cells and adipocytes plays an important role in the regulation of host metabolism [27.Priyadarshini M. et al.SCFA Receptors in pancreatic beta cells: novel diabetes targets?.Trends Endocrinol. Metab. 2016; 27: 653-664Abstract Full Text Full Text PDF PubMed Scopus (57) Google Scholar, 28.Ge H. et al.Activation of G protein-coupled receptor 43 in adipocytes leads to inhibition of lipolysis and suppression of plasma free fatty acids.Endocrinology. 2008; 149: 4519-4526Crossref PubMed Scopus (328) Google Scholar, 29.Gao Z. et al.Butyrate improves insulin sensitivity and increases energy expenditure in mice.Diabetes. 2009; 58: 1509-1517Crossref PubMed Scopus (1098) Google Scholar] – for example, via butyrate- and propionate-stimulated secretion of glucagon-like peptide 1 (GLP-1) and the appetite-regulating hormone PYY in intestinal enteroendocrine cells [30.Psichas A. et al.The short chain fatty acid propionate stimulates GLP-1 and PYY secretion via free fatty acid receptor 2 in rodents.Int. J. Obes. 2015; 39: 424-429Crossref PubMed Scopus (343) Google Scholar, 31.Kaji I. et al.Short-chain fatty acid receptor and its contribution to glucagon-like peptide-1 release.Digestion. 2014; 89: 31-36Crossref PubMed Scopus (85) Google Scholar, 32.Chambers E.S. et al.Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults.Gut. 2015; 64: 1744-1754Crossref PubMed Scopus (557) Google Scholar]. Enteroendocrine cells also release GLP-2 in response to parenteral nutrition with butyrate, increasing plasma concentrations of GLP-2 [26.Tappenden K.A. et al.Glucagon-like peptide-2 and short-chain fatty acids: a new twist to an old story.J. Nutr. 2003; 133: 3717-3720Crossref PubMed Scopus (68) Google Scholar,33.Akiba Y. et al.Short-chain fatty acid sensing in rat duodenum.J. Physiol. 2015; 593: 585-599Crossref PubMed Scopus (48) Google Scholar]. GLP-2 increases the surface area of epithelial in the small intestinal by enhancing proliferation and inhibiting apoptosis in both humans and piglets [26.Tappenden K.A. et al.Glucagon-like peptide-2 and short-chain fatty acids: a new twist to an old story.J. Nutr. 2003; 133: 3717-3720Crossref PubMed Scopus (68) Google Scholar,34.Jeppesen P.B. Teduglutide, a novel glucagon-like peptide 2 analog, in the treatment of patients with short bowel syndrome.Ther. Adv. Gastroenterol. 2012; 5: 159-171Crossref PubMed Scopus (60) Google Scholar]. GLP-2 also upregulates expression of the transporters for glucose, dipeptides, and amino acids in intestinal epithelial cells [35.Sangild P.T. et al.Glucagon-like peptide 2 stimulates intestinal nutrient absorption in parenterally fed newborn pigs.J. Pediatr. Gastroenterol. Nutr. 2006; 43: 160-167Crossref PubMed Scopus (46) Google Scholar]. These effects of SCFAs most likely explain the intestinal enteropathy associated with starvation and the beneficial effects of prebiotic fiber on intestinal function. GPCRs binding SCFAs are also expressed on intestinal enterocytes and other cell types in organs and tissues such as the liver, muscle, enteric neurons, and also in immune cells – indicating the breadth of their potential interactions throughout the body [36.Gelis L. et al.Functional characterization of the odorant receptor 51E2 in human melanocytes.J. Biol. Chem. 2016; 291: 17772-17786Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar,37.Priori D. et al.The olfactory receptor OR51E1 is present along the gastrointestinal tract of pigs, co-localizes with enteroendocrine cells and is modulated by intestinal microbiota.PLoS One. 2015; 10e0129501Crossref PubMed Scopus (35) Google Scholar]. GPCR41 is highly expressed on sympathetic neuronal ganglia – in particular, the superior cervical ganglion (SCG) which controls energy expenditure via neural and hormonal effects on glucose and fat metabolism. GPCR41 is most abundantly expressed on the SCG during embryonic (E13.5 and E15.5) and postnatal (P1) stages but also in the sympathetic nervous system (SNS) of adult mice and humans [38.Kimura I. et al.Short-chain fatty acids and ketones directly regulate sympathetic nervous system via G protein-coupled receptor 41 (GPR41).Proc. Natl. Acad. Sci. U. S. A. 2011; 108: 8030-8035Crossref PubMed Scopus (506) Google Scholar]. GPCR41−/− mice have no growth differences to wild-type (WT) mice or abnormalities in metabolic parameters and hormones, but during development the SCG volume is significantly smaller than it is in WT mice, indicating that GPCR41 may be involved in sympathetic nerve growth [38.Kimura I. et al.Short-chain fatty acids and ketones directly regulate sympathetic nervous system via G protein-coupled receptor 41 (GPR41).Proc. Natl. Acad. Sci. U. S. A. 2011; 108: 8030-8035Crossref PubMed Scopus (506) Google Scholar]. These authors found that propionate promotes GPCR41-mediated SNS activation whereas β-hydroxybutyrate, a major ketone body produced during starvation, depresses activation of sympathetic neuronal ganglia. These findings indicate that SCFAs and ketone bodies control energy balance by directly regulating GPCR41-mediated sympathetic activation. Fatty acid signaling through GPCRs expressed on immune cells is also important in immune regulation. GPCR43-deficient mice have exacerbated or unresolving inflammation in experimentally induced models of colitis, arthritis, and asthma [39.Maslowski K.M. et al.Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43.Nature. 2009; 461: 1282-1286Crossref PubMed Scopus (1887) Google Scholar]. GRPR41 but not GRP43, was also shown to be necessary for the protective effect of propionate in an induced allergic airway disease mouse model [40.Trompette A. et al.Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis.Nat. Med. 2014; 20: 159-166Crossref PubMed Scopus (1379) Google Scholar]. In the colon mucosa, vitamin B3 or butyrate binding to GPCR109A on antigen-presenting cells (APCs) induces an anti-inflammatory expression program in colonic APCs, which, in turn, induces differentiation of interleukin-10 (IL-10)-producing T regulatory cells (Tregs) [41.Singh N. et al.Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis.Immunity. 2014; 40: 128-139Abstract Full Text Full Text PDF PubMed Scopus (1019) Google Scholar]. The epigenome describes the modifications to the genome that do not affect the DNA sequence but lead to altered gene expression. Epigenetic modifications include DNA methylation and histone modification which alter how the DNA is packaged into chromatin (Box 1) [42.Lee K.K. Workman J.L. Histone acetyltransferase complexes: one size doesn't fit all.Nat. Rev. Mol. Cell Biol. 2007; 8: 284-295Crossref PubMed Scopus (716) Google Scholar,43.Roth S.Y. et al.Histone acetyltransferases.Annu. Rev. Biochem. 2001; 70: 81-120Crossref PubMed Scopus (1520) Google Scholar].Box 1Post-translational Modifications in the Histone Tails Enable Epigenetic RegulationChromatin comprises nucleosomes in which the DNA is wound around a central histone H3/H4 tetramer sandwiched between two histone H2A/H2B dimers. Adjacent nucleosomes are joined by a stretch of free linker DNA [92.Felsenfeld G. Groudine M. Controlling the double helix.Nature. 2003; 421: 448-453Crossref PubMed Scopus (792) Google Scholar]. Further compaction is possible through the linking interaction of histone 1 proteins between nucleosomes. Condensed chromatin is generally limiting access of the transcription machinery to the DNA but can undergo relaxation in response to specific cellular and environmental signals to allow for DNA replication and transcription [93.Grunstein M. Histone acetylation in chromatin structure and transcription.Nature. 1997; 389: 349-352Crossref PubMed Scopus (2310) Google Scholar, 94.Arrowsmith C.H. et al.Epigenetic protein families: a new frontier for drug discovery.Nat. Rev. Drug Discov. 2012; 11: 384-400Crossref PubMed Scopus (987) Google Scholar, 95.Berger S.L. et al.An operational definition of epigenetics.Genes Dev. 2009; 23: 781-783Crossref PubMed Scopus (1116) Google Scholar] (Figure I).The accessible regions of histones, called histone tails, protrude from the nucleosome and undergo post-translational modifications (PTMs) such as acetylation, methylation, ubiquitination, and other modifications generating what is commonly referred to as 'the histone code'. The PTMs determine whether the chromatin is repressing or activating transcription. Acetylation of histone tails is carried out by histone acetyltransferase (HATs [43.Roth S.Y. et al.Histone acetyltransferases.Annu. Rev. Biochem. 2001; 70: 81-120Crossref PubMed Scopus (1520) Google Scholar]) and reversed by histone deacetylases (HDACs). Acetylation of histone tails causes relaxation of chromatin through disruption of the DNA histone interaction, potentially activating transcription [96.Chen J. et al.The relation of histone acetylation/deacetylation and DNA methylation.Sheng Li Ke Xue Jin Zhan. 2001; 32: 362-364PubMed Google Scholar,97.Berger S.L. The complex language of chromatin regulation during transcription.Nature. 2007; 447: 407-412Crossref PubMed Scopus (2024) Google Scholar]. Conversely, removal of the acetyl groups by HDACs is considered to promote stronger histone–DNA associations. There are 18 known HDACs that are classified into four groups based on homologies and location. HDACs have also been shown to deacetylate more than 50 transcription factors and nonhistone targets, greatly extending their regulatory functions [98.Choudhary C. et al.Lysine acetylation targets protein complexes and co-regulates major cellular functions.Science. 2009; 325: 834-840Crossref PubMed Scopus (2911) Google Scholar, 99.Sun H. et al.Epigenetics of the depressed brain: role of histone acetylation and methylation.Neuropsychopharmacology. 2013; 38: 124-137Crossref PubMed Scopus (246) Google Scholar, 100.You S.H. et al.The interaction between nuclear receptor corepressor and histone deacetylase 3 regulates both positive and negative thyroid hormone action in vivo.Mol. Endocrinol. 2010; 24: 1359-1367Crossref PubMed Scopus (43) Google Scholar]. Chromatin comprises nucleosomes in which the DNA is wound around a central histone H3/H4 tetramer sandwiched between two histone H2A/H2B dimers. Adjacent nucleosomes are joined by a stretch of free linker DNA [92.Felsenfeld G. Groudine M. Controlling the double helix.Nature. 2003; 421: 448-453Crossref PubMed Scopus (792) Google Scholar]. Further compaction is possible through the linking interaction of histone 1 proteins between nucleosomes. Condensed chromatin is generally limiting access of the transcription machinery to the DNA but can undergo relaxation in response to specific cellular and environmental signals to allow for DNA replication and transcription [93.Grunstein M. Histone acetylation in chromatin structure and transcription.Nature. 1997; 389: 349-352Crossref PubMed Scopus (2310) Google Scholar, 94.Arrowsmith C.H. et al.Epigenetic protein families: a new frontier for drug discovery.Nat. Rev. Drug Discov. 2012; 11: 384-400Crossref PubMed Scopus (987) Google Scholar, 95.Berger S.L. et al.An operational definition of epigenetics.Genes Dev. 2009; 23: 781-783Crossref PubMed Scopus (1116) Google Scholar] (Figure I). The accessible regions of histones, called histone tails, protrude from the nucleosome and undergo post-translational modifications (PTMs) such as acetylation, methylation, ubiquitination, and other modifications generating what is commonly referred to as 'the histone code'. The PTMs determine whether the chromatin is repressing or activating transcription. Acetylation of histone tails is carried out by histone acetyltransferase (HATs [43.Roth S.Y. et al.Histone acetyltransferases.Annu. Rev. Biochem. 2001; 70: 81-120Crossref PubMed Scopus (1520) Google Scholar]) and reversed by histone deacetylases (HDACs). Acetylation of histone tails causes relaxation of chromatin through disruption of the DNA histone interaction, potentially activating transcription [96.Chen J. et al.The relation of histone acetylation/deacetylation and DNA methylation.Sheng Li Ke Xue Jin Zhan. 2001; 32: 362-364PubMed Google Scholar,97.Berger S.L. The complex language of chromatin regulation during transcription.Nature. 2007; 447: 407-412Crossref PubMed Scopus (2024) Google Scholar]. Conversely, removal of the acetyl groups by HDACs is considered to promote stronger histone–DNA associations. There are 18 known HDACs that are classified into four groups based on homologies and location. HDACs have also been shown to deacetylate more than 50 transcription factors and nonhistone ta