Huntington patients and both mouse and  Drosophila  models show histone H3 and H4 hypoacetylation.  There are currently no treatments for the disease but numerous HDAC inhibitors have been tested and shown to reverse the certain symptoms caused by the Htt mutation.


Parkinson's disease (PD) is characterized by progressive degeneration of dopaminergic neurons in the substantia nigra by causes unknown.  Several genes and environmental factors (e.g. pesticide exposure) may play a role in onset of PD.  Hallmarks include mutations to the alpha-synuclein gene,  SNCA , as well as  PARK2 ,  PINK1 ,  UCHL1 ,  DJ1 , and  LRRK2  genes, and fibrillar accumulation of  Lewy bodies  from misfolded alpha-synuclein. Symptoms are most noticeably manifested in disorders of movement, including shaking, rigidity, deficits in making controlled movements, and slow and difficult walking.  The late stages of the disease result in dementia and depression. Levodopa and dopaminergic therapy may ameliorate symptoms, though there is no treatment to halt progression of the disease.


Epigenetic treatments tested in models of PD are few, though some promising research has been conducted.  Most treatments investigated thus far are directed at histone modifications and analysis of their roles in mediating alpha-synuclein expression and activity.  Pesticides and paraquat increase histone acetylation, producing neurotoxic effects similar to those seen in PD, such as apoptosis of dopaminergic cells. [ 115 ]  Despite this, treatment with HDACis [ 116 ]  seems to have a neuroprotective effect.


Multiple sclerosis (MS) is a demyelinating neurodegenerative disease that does not have a confirmed cause, but is widely considered to be an autoimmune disease in nature. [ 117 ]  It is indicated by demyelination of the nerves of the brain and spinal cord. Its symptoms are unique in nature and vary, but include those that have degenerative effects in the eyes and limbs. These can present themselves as numbness or atrophy, shock like sensations, paralysis, as well as lack of coordination or tremors, within the extremities. Within the eye, multiple sclerosis can cause blurriness, double vision, pain, or vision loss. Multiple sclerosis effects can be presented throughout other realms of the body, but is largely characterized by these main symptoms. Some of these can include loss of sexual or excretory function and epilepsy. While there are a few subcategories of multiple sclerosis, in most instances, the disease afflicts in a relapsing nature, where relapses of symptoms might not occur for extended periods of time, yielding more to the uncertainty of the disease. There is no known cure for MS, but measures can be taken post relapse to regain loss of function and the symptoms can be mitigated via therapeutic or medicinal means. [ 118 ]


Because of the outside factors that precede multiple sclerosis and the heritability typically occurring within the mother, it is thought to have an epigenetic cause. Some factors that may increase the incidence of MS are smoking, vitamin deficiency, and a history of some viral infections—which are factors that can induce epigenetic change. [ 119 ]


Human leukocyte antigen-DRB1*15 haplotype is a potential risk factor of MS. Because of the increased likelihood of the mother's human leukocyte antigen-DRB1*15 allele being passed onto their children, this contributes to the instances of MS being more prevalent from the mother. HLA-DRB1 is thought to be regulated via epigenetic means. The correlation of MS and this allele is speculated to be due to the presence of hypomethylation in the CpG island of HLA-DRB1, and those that carry the allele tend to exhibit this hypomethylation. HLA-DRB1 exon 2 is a particular region where evidence has shown that methylation is shown to be important in regulation. Research has furthered the evidence that variation in HLA-DRB1 DMR, which is a mechanism that is methylation regulated, that in turn regulates increased HLA-DRB1 expression, displays an increased risk for MS, and the exhibition of the disease. [ 119 ] [ 120 ]


Higher levels of expression of specific types of miRNA are often seen in the brain of those afflicted, showing an association of these types of miRNA and MS. Higher expression of miR-155 and miR-326 is often associated with CD4+T cell differentiation, and with this differentiation, instances of autoimmune encephalitis occur, which is the link with which it is thought that smoking can induce epigenetic changes that increase susceptibility to MS. Higher expression levels of miR-18b, miR-493, miR-599, and miR-96 are often seen in patients diagnosed with MS. miR-145 detection appears to be a promising future diagnostic tool due to its high specificity of 90% and sensitivity of 89.5% in whole blood testing due to its capability of distinguishing healthy patients versus those with MS. A symptom associated with MS patients is white matter lesions in the brain, and these lesions when biopsied showed higher expression of miR-155, miR-326 and miR-34a. These are especially notable due to the fact that overexpression of these miRNA's cause downregulation of CD47, leading to myelin phagocytosis, because of CD47's role of inhibiting macrophage activity. [ 121 ]


MS patients can be identified through observation of abnormal DNA methylation patterns in genes responsible for inflammation and myelination factor expression. Methylation occurs in the genomic region, CpG island, and is imperative in regulation of transcription. A methylated CpG region typically is the mechanism that will silence a gene, whereas a hypomethylated region is able to induce transcription. Using methylation inhibitors it has been shown that allowing higher proliferation of T cells can be achieved by preventing silencing. Abnormalities in methylation patterns increase the generation of CD4+T auto reactive. Hypomethylation of CpG regions of the PAD2 gene, a regulator of MBP which in turn regulates myelin, is also associated with higher instances of MS. This hypomethylation leads to overexpression of the PAD2 gene. These patterns have been observed in the white matter of patients with MS. While methylation is an indicator of MS, its effects are more specialized to location in MS, for example, where these patterns are observed in white matter. [ 121 ]


Association of abnormal histone modification in MS patients can be found in lesions located in the brain, with most instances of this being observed in patients over time and in lesions located in the frontal lobe. Higher instance of histone acetylation can be seen in patients afflicted over time, but this is counteracted by lower instances of histone acetylation in lesions found on the brain early in the course of the disease. The mechanisms by which histone modifications work in the progression of MS are unconfirmed, but changes in acetylation are often associated with the disease.


Trichostatin


Positive responses were observed in animal trials utilizing this HDAC inhibitor, associated with mediation of inflammatory pathways and thus resulting in lower instances of inflammatory responses in the brain. It was also shown to be effective in decreasing levels of disability when the mice were in a relapsing stage of MS. Trichostatin's mediation of symptoms is not well known but is thought to work in increasing acetylation at the H3 and H4 histones in CD4+T cells where MS patients often display differences in acetylation levels at these histones that control patients do not.


Vorinostat


Animal trials were utilized along with the testing of human myeloid dendritic cells. Not much is known about the mechanisms of vorinostat; however regulation of Th1/Th17 cytokine expression, which are responsible for inducing inflammation, were observed, thereby decreasing instances of inflammation and demyelination. Decreased patterns of T cell proliferation were also observed, similar to how trichostatin mediates disease symptoms. [ 122 ]


Valpropic acid


Valpropic acid has been shown to have positive results in animal trials, in the mitigation of the disease by regulating the severity and duration of MS. Its mechanism is decreasing the presentation of miRNA. Its mechanism for such has been observed in rats by shifting Th1 and Th17 to Th2 (responsible for inducing inflammation), thereby downregulating miRNA expression in inflammatory cytokines, tumor mediating mechanisms, and the spine. This is another instance in which T cell expression regulation is present, by preventing proliferation through interference of its pathway, similar to trichostatin and vorinostat. Another effect of VPA is its prevention of macrophage and lymphocyte proliferation in the spinal cords of MS rats. Currently, no HDAC inhibitors are in use for the mitigation of symptoms in MS patients; however, some are in pre-clinical trials at this time. [ 121 ]


Epigenetics of physical exercise  is the study of epigenetic modifications to the cell genome resulting from physical exercise. Environmental factors, including physical exercise, have been shown to have a beneficial influence on epigenetic modifications. Generally, it has been shown that acute and long-term exercise has a significant effect on DNA methylation, an important aspect of epigenetic modifications.


The broader field of epigenetics studies heritable alterations to genes that do not involve changing the DNA sequence itself. The next section briefly discusses two important mechanisms involved in epigenetic modifications.


Epigenetic modifications such as DNA methylation and histone modifications alter DNA accessibility and change chromatin structure, thereby regulating patterns of gene expression. [ 1 ]  These modifications can be heritable, thus passing from parent to offspring.


As mentioned previously, environmental factors can modulate epigenetic alterations. Factors such as diet, exposure to environmental toxins, and stress have all been shown to play a role in affecting epigenetic modifications, especially by influencing methylation patterns in the DNA. [ 2 ]  Physical exercise is one such factor that also has been shown to affect methylation and chromatin modifications.


DNA methylation occurs when a methyl group is covalently attached to the C5 position of a cytosine nucleotide by a DNA methyltransferase (DNMT) enzyme. These dinucleotide repeats where cytosine is followed by an adjunct guanine nucleotide are referred to as CpG sites, with the 'p' indicating a phosphodiester linkage. Parts of the genome that contain a high amount of CpG sites are named CpG islands, and these islands often overlap with many of the core promoter regions found in the human genome. [ 3 ]  There are also CpG sites that are not a part of CpG islands, and these are constitutively methylated to indicate to transcription machinery to not allow transcription to be initiated there. In contrast, CpG islands are the areas in the genome where CpG sites are usually unmethylated until DNMTs methylate them, resulting in effects on gene expression.


The methylation of CpG islands typically results in the transcriptional silencing of a promoter, which can be done in two ways. Methylation can recruit histone deacetylases (HDAC), which work to form tightly condensed heterochromatin, which is transcriptionally inactive. Methylating a CpG island will also cause the methyl group to wedge into the DNA major groove, effectively blocking binding sites for proteins that can activate transcription.


Histones are proteins that help organize DNA. Eight histone proteins assemble into an octomer that DNA wraps around to create a unit called a nucleosome. The ability of a histone to be modified by being marked on its N-terminal tail is essential for modulating gene expression. [ 5 ]  In its most basic sense, histones can be modified to become more or less condensed by histone deacetylases (HDACs) or histone acetyltranferases (HATs), respectively. When histones are acetylated and become less condensed as a result, it allows for the underlying DNA to be more accessible to be transcribed, increasing gene expression. Thus, acetylated histones can serve as binding sites for important transcription initiation factors and enzymes that have the ability to remodel chromatin. Meanwhile, increased condensation of histones via deacetylation results in the opposite effect, causing decreased gene expression. The regulation of gene expression can have implications on which genes are transcribed, ultimately affecting protein production in the human body.


Though histone tails can be marked in many different ways, four prominent modifications will be discussed in this article: acetylation, methylation (of histones), ubiquination, and phosphorylation. [ 1 ]


In addition, methylated histones can both serve as binding sites for certain transcription factors due to their bromodomains and chromodomains, and also prevent the binding of such factors by hiding the recognition site of the transcription factor. [ 6 ]  Transcription factors, including promoters and enhancers, can subsequently modulate the rate at which DNA is transcribed to RNA, also affecting gene expression.


Exercise of the human  vastus lateralis  (a thigh muscle) primarily affects the  epigentic  status of sites in  enhancers  within muscle cell  chromatin , as described in detail below.  In contrast, exercise of this  skeletal muscle  causes few or no epigenetic alterations in  promoters  or within  genes  of muscle cell chromatin. [ 7 ] [ 8 ]


Skeletal muscles are substantially composed of very large,  multinucleated , contractile  muscle fiber cells  (myocytes). However, considerable numbers of small resident and infiltrating mononuclear cells are also present in skeletal muscles. [ 9 ]   In terms of volume, myocytes make up the great majority of skeletal muscle.  However, in terms of nuclei present in skeletal muscle, myocyte nuclei may be only half of the nuclei present, while nuclei from resident and infiltrating mononuclear cells make up the other half. [ 9 ]


Mononuclear cells found in skeletal muscle tissue samples from mice and humans [ 11 ] [ 12 ] [ 10 ]  can be identified by  messenger RNA  transcription of cell type markers. Cameron et al. [ 10 ]  identified nine cell types in skeletal muscles.  They include  endothelial cells  (45% of cells), fibro-adipogenic progenitors (FAPs)(20%), [ 13 ]   pericytes  (14%) and endothelial-like pericytes (4%). Another 9% of mononuclear cells are  muscle stem cells , adjacent to muscle fiber cells. Types of  lymphoid cells  (such as B-cells and T-cells) (3%) and myeloid cells such as  macrophages  (2%) make up most of the remaining mononuclear cells of skeletal muscle. [ 10 ]  In addition,  Cameron et al. [ 10 ]  also identified two types of myocyte cells, Type I and Type II. Each of the different types of cells in skeletal muscle was found to express different sets of genes. The median number of genes expressed in each of the nine different cell types was 1,331 genes. When a biopsy is taken from a thigh muscle, however, the biopsy contains all the different cell types. Mixed together, in a biopsy of human thigh skeletal muscle, there are 13,026 to 13,108 genes with detected expression. [ 14 ] [ 8 ]


The functions of skeletal muscle include producing movement, maintaining body posture, controlling body temperature, and stabilizing joints. [ 15 ]  Skeletal muscle is also an  endocrine organ . [ 16 ] [ 17 ] [ 18 ]  Under different physiological conditions, subsets of 654 different proteins as well as lipids, amino acids, metabolites and small RNAs are found in the  secretome  of skeletal muscles. [ 19 ]   A secretome is secreted by skeletal muscle cells, either locally (in skeletal muscle interstitium) or into the blood circulation, with a measurable plasma concentration. [ 20 ]  Secreted proteins often have an  endocrine  effect. [ 21 ]


Williams et al. [ 8 ]  obtained biopsies of  a thigh skeletal muscle  (vastus lateralis muscle) of eight 23-year-old, originally sedentary, Caucasian males. Biopsies were taken both before and after a six-week-long endurance exercise training program. The exercise consisted of riding a stationary bicycle for one hour five days a week for six weeks.


Of the 13,108 genes with detected expression in the muscle biopsies, 641 genes were upregulated after endurance training and 176 genes were downregulated. Of the 817 genes whose expression was altered, 531 were identified as being in the secretome of skeletal muscle. Because many of the exercise-regulated genes are identified as secreted, this indicates that much of the effect of exercise has an endocrine rather than metabolic function. [ 8 ]  The main pathways found to be affected by secreted exercise-regulated proteins were related to  cardiac ,  cognitive ,  kidney  and  platelet  functions.


Between 2012 and 2019 at least 25 reports indicated a major role of  epigenetic  mechanisms in skeletal muscle responses to exercise. [ 22 ]  Epigenetic alterations often occur by  adding methyl groups to cytosines in the DNA  or  removing methyl groups from the cytosines of DNA , especially at  CpG sites  within enhancers. Methylations of cytosines can cause the DNA to be compacted into  heterochromatin , thus inhibiting access of other molecules to the DNA. [ 23 ]  Epigenetic alterations also often occur through acetylations or deacetylations of the  histone  tails within  chromatin . DNA in the nucleus generally consists of segments of 146  base pairs  of DNA wrapped around eight tightly connected  histones  (and each histone also has a loose tail) in a structure called a  nucleosome  and one segment of DNA is connected to an adjacent DNA segment on a nucleosome by  linker DNA . When histone tails are  acetylated  they usually cause loosening of the DNA around the nucleosome, leading to increased accessibility of the DNA.


Gene expression  in muscle is largely regulated, as in tissues generally, by  regulatory DNA sequences , especially  enhancers . Enhancers are non-coding sequences in the genome that activate the expression of distant target genes, [ 24 ]  by looping around and interacting with the  promoters  of their target genes [ 25 ]  (see Figure "Regulation of transcription in mammals"). As reported by Williams et al., [ 8 ]  the average distance in the loop between the connected enhancers and promoters of muscle genes is 239,000 nucleotide bases.


Endurance muscle training alters muscle gene expression by epigenetic  DNA methylation  or de-methylation of  CpG sites  within enhancers. [ 7 ]


In a study by Lindholm et al., [ 7 ]  twenty-three individuals who were about 27 years old and sedentary volunteered to have  endurance training  on only one leg during 3 months. The other leg was used as an untrained control leg. The training consisted of one-legged knee extension training for 3 month (45 min, 4 sessions per week). Skeletal muscle biopsies from the  vastus lateralis  (a thigh muscle) were taken both before training began and 24 hours after the last training session from each of the legs. The endurance-trained leg, compared to the untrained leg, had significant  DNA methylation  changes at 4,919 sites across the genome. The sites of altered DNA methylation were predominantly in  enhancers . Transcriptional analysis, using  RNA sequencing , identified 4,076 differentially expressed genes.


The  transcriptionally upregulated genes  were associated with enhancers that had a significant decrease in  DNA methylation , while transcriptionally downregulated genes were associated with enhancers that had increased DNA methylation. Increased methylation was mainly associated with genes involved in structural remodeling of the muscle and glucose metabolism. Enhancers with decreased methylation were associated with genes functioning in inflammatory or immunological processes and in transcriptional regulation.


As indicated above, after exercise,  epigenetic  alterations of  enhancers  alter long-term  expression  of hundreds of muscle genes. [ 8 ]  This includes genes producing proteins secreted into the systemic circulation, many of which may act as endocrine messengers. [ 8 ]  Six sedentary, about 23 years old, Caucasian males provided  vastus lateralis  (a thigh muscle) biopsies before entering an exercise program (six weeks of 60-minute sessions of riding a stationary cycle, five days per week). Four days after this exercise program was completed, the expression of many genes was persistently  epigentically  altered. The alterations included acetylations and deacetylations of the histone tails located in the enhancers controlling the genes with altered expression. [ 8 ]


Up-regulated genes were associated with epigenetic acetylations of histone 3 lysine 27 (H3K27ac) of nucleosomes located at their  enhancers . Down-regulated genes were associated with the removal of epigenetic acetylations at H3K27 in nucleosomes located at their enhancers (see Figure "A  nucleosome  with  histone  tails set for transcriptional activation"). Biopsies of the vastus lateralis muscle showed expression of 13,108 genes at baseline before the exercise training program. Four days after the exercise program was completed, biopsies of the same muscles showed altered gene expression, with 641 genes up-regulated and 176 genes down-regulated. [ 8 ]  Williams et al. identified 599 enhancer-gene interactions, covering 491 enhancers and 268 genes (multiple enhancers were found connected to some genes), where both the enhancer and the connected target gene were coordinately either upregulated or downregulated after exercise training. [ 8 ]


Physical exercise leads to epigenetic modifications that can have beneficial effects in cancer patients. The effect of physical exercise on DNA methylation patterns leads to increased expression of genes associated with tumor suppression and decreased expression of oncogenes. Cancer cells have non-normal patterns of DNA methylation including hypermethylation in promoter regions for  tumor-suppressing genes  and hypomethylation in promoter regions of oncogenes. [ 6 ]  These epigenetic mutations in cancer cells cause the cell to grow and divide uncontrollably, resulting in tumorigenesis. Physical exercise has been shown to reduce and even reverse these epigenetic mutations, increasing expression levels of tumor-suppressing genes and decreasing expression levels of oncogenes.


Hypermethylation in the promoter regions of tumor suppressor genes is thought to help cause some forms of cancer. The hypermethylation in the promoter regions of the tumor suppressing genes APC and RASSF1A are common epigenetic markers for cancer. [ 26 ]  The APC gene functions to make sure cells divide properly and maintain a correct number of chromosomes after division has completed. The RASSF1A gene product interacts with the DNA repair protein XPA. Physical exercise has been shown to decrease and even reverse these promoter hypermethylation, lowering the risk of the development of cancer. [ 26 ]  Decreased hypermethylation patterns reveal a transcriptionally accessible promoter region, allowing for increased expression of the tumor suppressing genes.


Physical exercise increases levels of eustress, or good stress, on the body. This eustress stimulates epigenetic modifications affecting the DNA genome of cancer cells. [ 27 ]  Environmental conditions, such as eustress, strongly induces expression of the tumor suppressor TP53 gene by influencing epigenetic modifications to be made to the cancer cells genome. [ 27 ]  The TP53 gene codes for the p53 protein, a protein important in the apoptotic pathway of programmed cell death. The p53 protein is important for the regulation of cell growth and apoptosis, so hypermethylation of the TP53 promoter region are common markers associated with the development of cancer. Other than methylation patterns affecting expression of TP53,  microRNAs  and antisense RNAs control the levels of the p53 protein by regulating expression of the p53 coding TP53 gene. [ 27 ]


In a study on the epigenetic effects of physical exercise on breast cancer in women, blood samples from breast cancer patients were collected before and after 6 months of moderate-intensity aerobic exercise. [ 28 ]  The test group experienced 129 minutes of exercise on average per week compared to the control group’s 21.8 minutes a week. The study found 43 genes having significant changes in DNA methylation. Of the 43 genes, 3 of the genes experiencing reduced methylation levels were directly correlated with increased survival of breast cancer. The gene L3MBTL1, a known tumor suppressor, had methylation levels decreased by 1.48% in the exercise group while the limited exercise control group experienced a 2.15% increase in methylation. [ 28 ]  The 1.48% decrease in methylation of L3MBTL1 resulted in greater expression of the tumor suppressor while the 2.15% increase in methylation experienced by the limited exercise control group led to a decrease in expression. The findings of the study showed patients who exercised regularly had lower methylation levels and higher gene expression of L3MBTL1. [ 28 ]  These patients also experienced a greater than 60% reduction in risk of breast cancer death compared to patients in the limited exercise group. [ 28 ]


Epigenetic mechanisms affected by physical exercise have also been seen to be involved in age-related processes. A major component of aging is significant loss of DNA methylation over time. [ 29 ]  Methyl deoxycytidine, which is a methylated  cytosine  on the 5’ carbon of a cytosine, is involved in the process of  cell differentiation  and maintenance. Cell differentiation involves methylation of different areas within the DNA of a cell, which can alter the transcription of genes. During cell differentiation, DNA methylation is important for establishing the identity and function of a cell because of its role in controlling gene expression. A recent study looking at genome DNA methylation of newborn infants and humans aged 100 years or older found that the older individuals had significantly decreased overall DNA methylation. [ 30 ]  As one ages, the amount of DNA methylation slowly begins to decrease.


Studies have also looked at methyl deoxycytidine residues from tissues collected from rodents at various ages. These studies found that DNA methylation loss increased significantly as the rodent aged. [ 29 ]  Thus, aging is related to a significant loss in DNA methylation. [ 29 ] [ 30 ]  However, this loss of DNA methylation appears to be slowed by physical exercise under rare conditions, in general this effect is not very well studied and so far it seems like there is no connection between DNA methylation and physical activity. [ 31 ]  Further studies have looked at the effects of physical exercise on DNA methylation and aging in humans.


Another component of aging is the gradual shortening of telomeres located at the end of chromosomes.  Telomeres  are repetitive sequences located at the end of chromosomes whose purpose are to slow the process of shortening and cell damage which occurs after every cell division as well as stabilize the ends of DNA. Aging and age-related diseases are associated with the significant  shortening  of these sequences. The shrinking of telomeres occurs in somatic cells where telomerase, the enzyme in control of telomere lengthening, is not expressed. [ 32 ]


However, it has been seen that telomeres can transcribe  non-coding RNA , or functional RNAs that do not get translated into protein. Research has demonstrated that some of the non-coding RNAs transcribed at telomeres are involved in heterochromatin formation and stability of the telomeres. [ 30 ] [ 33 ]  These non-coding RNAs can be positively impacted by physical exercise. Notably, a study found that mice exposed to short-term running phases had increased non-coding RNA transcription at telomeres as compared to sedentary controls. [ 34 ]  This increase in non-coding RNA transcription aided telomere stability, making the exercise group's telomeres less likely to be as affected by aging over time. Through helping to increase telomere stability, physical exercise can have positive impacts on aging by helping to decreasing the shortening of telomeres.


In addition to restructuring the muscular and skeletal system to better handle mechanical stress, physical exercise also affects gene expression with respect to metabolism. The effects are widespread and can affect anything from muscle growth to aerobic stamina to diabetes and other metabolic disorders. [ 35 ]


In general, even a small amount of exercise can induce hypomethylation of the whole genome within muscle cells. This means that many regulatory genes can be turned on for pathways like muscle repair and growth. The intensity of the exercise directly correlates to the amount of promoter demethylation, so more strenuous exercise activates more genes. [ 35 ]


MicroRNAs (miRNAs) interfere with mRNA that is present and render it unusable and therefore decrease the product of that mRNA. MiRNAs regulate many physiological processes, such as inflammation, angiogenesis (the creation of blood vessels), as well as ischemia (the restriction of blood flow within the vessels) prevention. Aerobic exercise reduces the overall number of various miRNAs within the skeletal muscle that produce negative effects. Stimuli that cause the body to enter an anabolic, or constructive, phase, such as resistance training as well as the correct diet, has also shown a reduction of miRNAs. This reduction may actually play a role in the growth of the muscle cell. [ 35 ]


Class IIa Histone deacetyltransferases ( HDACs ) are highly expressed within human skeletal muscles. Exercise helps to reduce their activity, especially at promoters, which affects gene expression. In mice, this regulation of HDAC5 has been shown to increase the amount of type I fibers in muscle. Type I fibers are slow twitch, endurance fibers. This data agrees with human data that says the amount of type I fibers is positively correlated with the maximal aerobic capacity.


It also suggested that the amount of type 1 fibers is correlated with a histone acetyltransferase ( HAT ) that is involved in  osteoblast  differentiation and bone formation. [ 35 ]


Individuals with  type II diabetes  have hypermethylation of several genes within the muscle, like peroxisome proliferator-activated receptor gamma ( PPAR-γ ) and coactivator 1 alpha ( PGC-1α ). The hypermethylation of these genes decreases the expression of both mitochondrial DNA as well as PGC-1α mRNA. Exercise is a way to prevent and treat these effects by helping to hypomethylate PPAR-γ and PGC-1α. Additionally, exercise also increases expression of glucose transporter type 4 ( GLUT4 ), which will also help with diabetes symptoms. [ 35 ] [ 36 ]


Physical exercise can cause various types of epigenetic alterations, but there are four prominent types that affect  cognition  that will be discussed in this article. The other types of epigenetic alterations cannot be ruled out as not having an effect on cognition, but there is not much known about them yet. An extensive 2017 review [ 37 ]  describes effects of exercise on the brain due to (1)  DNA methylation , (2)  histone acetylation , (3)  histone methylation , and (4)  microRNA  expression, and the consequences of these alterations on learning and memory ( cognition ). Generally, the reviews found that exercise had positive effects on cognition, including enhanced cognitive function and the reversal of cognitive decline that typically happens during aging. Short-term effects of exercise were found to improve several cognitive abilities, such as cognitive flexibility and working memory, as well. The epigenetic mechanisms that act as a bridge between exercise and cognition are discussed below.


As summarized in the 2017 review, in rats, exercise enhances the expression of the gene  Bdnf , which has an essential role in memory formation.   Enhanced expression  of  Bdnf  occurs through demethylation of its  CpG island promoter  at  exon IV . Demethylation is implemented in part through the actions of  thymine-DNA glycosylase  and the  base excision repair system. [ 38 ]


Exercise decreases  hippocampus  expression of the gene-repressive  DNA methylating enzymes  DNMT1, DNMT3a and DNMT3b. The hippocampus has important functions in memory, spatial navigation and is part of the  reward system . Exercise also attenuates the global methylation changes induced by stress. [ 39 ]


Exercise has also been found to downregulate protein phosphatase1 (PP1) and calcineurin, both memory-suppressor genes. There is evidence that PP1 increases chromatin condensation through the action of dephosphorylating histone proteins, as well as by suppressing methylation and histone acetylation with the aid of HDACs. Additionally, Tet1, an important gene for memory formation, has been shown to be upregulated in response to two weeks of exercise. Concurrently, exercise also contributed to the demethylation of CpG islands found in the promoter region of gene VegfA, a growth factor that is known to modulate the positive effects that exercise can have towards the brain. [ 39 ]


Exercise causes  acetylation  of  histone H3  in the exon IV promoter region of the  Bdnf  gene essential for memory formation.  This acetylation contributes to upregulation of  Bdnf  in the brain hippocampi of rats. [ 40 ]   Two weeks of treadmill exercise improves memory performance in an inhibitory avoidance task. [ 37 ]


Histone methylation  can cause transcription repression. Lysine can undergo mono-, di- and tri-methylation.  Di- and tri-methylation of histone H3 at lysine 9 (H3K9) is related to transcription repression.  Mice deficient in a particular histone-methyltransferase gene,  KMT2A  (also known as MLL1), in adult excitatory neurons show impairments in hippocampus-dependent memory tasks. [ 41 ]   Aging induces decreases in the global methylation of H3K9 in the hippocampus. [ 37 ]   However, physical exercise counteracts the aging induced decreases in the global methylation of H3K9. [ 37 ]


MicroRNAs (miRNAs) have been discovered to be potential regulators of numerous biological processes within the brain, ranging from cell proliferation, differentiation, apoptosis, synaptic plasticity and memory formation, all very important processes involved in cognition. These miRNAs have also been found within the hippocampus, amygdala, and cortex, further linking its effects to memory formation and cognition. During their biogenesis, premature-miRNAs are exported from the nucleus to the cytoplasm. Subsequent processing of the pre-miRNA generates mature-miRNA, which binds to 3’UTR “seed sequence” of target mRNAs, a process that is catalyzed by the RNA-induced silencing complex (RISC). The binding of miRNA to the target mRNA can result in degradation of the target mRNA or inhibition of its translation into protein, with the degree of sequence complementarity between the miRNA and mRNA determining which mechanism is employed. Interestingly, each miRNA has the ability to interact with a large number of mRNAs (approximately 200–500 mRNA for each miRNA), suggesting that the majority of the protein-coding genes may be regulated by miRNAs. Therefore, it is not surprising that miRNAs are widely expressed in the brain, and that they can participate in epigenetic mechanisms. [ 42 ]


Eukaryotic cells can communicate directly with each other through cell–cell contact or at distance by secreting soluble factors such as hormones, growth factors, cytokines and chemokines. Both RNA and mRNAs can be functionally transferred from a donor to a recipient cell via membrane-derived vesicles called exosomes. Similarly to hormones, miRNAs are released into the circulation (called circulating miRNAs or c-miRNAs), to affect cells throughout the organism. The c-miRNAs are transported by exosomes, high-/low-density lipoproteins, apoptotic bodies, and RNA-binding proteins. A bout of exercise increases c-miR-223 levels in the circulation in young healthy men, while lack of miR-223 leads to hippocampal-dependent memory deficits and neuronal cell death. Likely arising from different mechanisms, both acute exercise and chronic endurance training have been shown to robustly modify the miRNA signature of human plasma. [ 37 ]


One pathway that involves miRNA is the CREB (cAMP responsive element binding protein) and BDNF (brain-derived neurotrophic factor) signaling pathway, a well known pathway activated by exercise. MicroRNA-132 (miR-132) is a miRNA that is regulated by CREB and is activated by neuronal activity and BDNF. MiR-132 levels are critical for memory development, with very low or high levels having a detrimental effect, and only moderate levels having a positive effect. It has been described that a single bout of acute intermittent exercise rapidly elevated circulating levels of miR-132 in young healthy men. More recently, it has been shown that conditional knockout of miR-132/212 gene cluster impairs memory and promotes gross alterations in hippocampal transcriptional profile in mice. Overall miR-132 is one of the most studied miRNAs in the context of exercise and is proven to be instrumental in multiple functions in the brain, including neuronal development, synaptic plasticity and memory formation. [ 39 ]


MiR-132 is but one of many miRNAs that are regulated by exercise. Microarray analysis shows a total of 32 miRNAs that are differentially expressed in the hypothalamus when subjected to physical activity. In addition, miR-21 and miR-34a have been shown to be regulated by exercise to reduce the harmful effects of brain injury and aging on cognition. Another miRNA, miR-124, known for its role in neurogenesis and memory formation, is also especially important to attenuate the effects of stress and is unregulated by exercise. Finally, physical exercise leads to altered miR clusters affecting increased cardiac angiogenesis in animal models. MiR-1, miR-133a, and miR-206 cluster levels were significantly elevated after exercise and correlated with performance parameters such as maximum oxygen uptake and anaerobic lactate threshold. [ 43 ]


Overall, exercise has been shown to alter blood levels of several miRNAs, and this indicates that exercise can use these epigenetic modulators to regulate communication between the brain and peripheral organs. With further knowledge of epigenetic pathways, exercise will continue to show its benefits in all phases of life including but not limited to cancer prevention and treatment, aging, metabolism and metabolic disorders like diabetes and cognition.


While it is easy to state that there is an inverse relationship between physical exercise and obesity, the reality—and scientific evidence—suggest otherwise. To start with a definition, obesity is the excess accumulation of fat within adipose tissue and is characterized by a body mass index (BMI) above 30. Obesity correlates with many cardiometabolic comorbidities such as cancer, cardiovascular conditions (stroke, heart failure), and various metabolic diseases. One of the methods of mitigating these effects is reduction of adipose tissue; this can be done by 2 methods—decreasing energy expenditure (physical exercise) or dietary modification. [ 44 ]


Research regarding the epigenetic effect of physical exercise on obesity is still in slightly uncharted. Much of the data that is collected simply compares epigenetic changes in patients that have been diagnosed as obese and patients that haven’t. However, this cannot discount the role of physical exercise and epigenetics as many of the epigenetic differences are correlated with BMI and waist circumference, both of which can be controlled via physical exercise. With that mentioned, since the research is new, there’s a plethora of information, much of which is unreviewed. Overall, the evidence for the effect of obesity on epigenetics lies in a specific set of genes that controls waist circumference(WC) and body mass index(BMI)--the evidence is not more concrete than this.


In a study that combined methylation data from 10,000 blood samples, 187 CpG sites were shown to be associated with BMI. [ 45 ]  What they found was highly interesting: deviations in DNA methylation in blood are usually assumed to be the result of obesity, and on some occasions, the cause. Using quantitative genetic analysis techniques, the researchers attempted to find either a causative or consequential relationship between the implicated genes and the obesity. They found that most of the interactions between the genes of interest and obesity were consequential—demonstrating that any alteration in gene activity is most likely the result of obesity, not a factor that caused it. This study was verified by testing within adipose tissue.


CD38 (cluster of differentiation 38) is a glycoprotein with enzymatic activity found on the surface of specific immune cells. The ectoenzyme has been shown to be important in nicotinic acid adenine dinucleotide phosphate ( NAADP ) synthesis. [ 46 ]  NAADP is an intracellular second messenger implicated in Ca 2+  release. When knocked-out in mice, the result was an increased metabolic rate and obesity resistance (induced by a high-fat diet). [ 47 ]  This tells us that CD38 is an important factor in the epigenetic change in regards to obesity. As found in an additional study, MSI2, a gene encoding the Musashi RNA-binding protein 2 was found to be associated with eating behavior. The same study found that LARS2 (mitochondrial gene) was implicated with BMI and waist circumference. [ 48 ]  In both cases, the researchers noted that for a +1 unit increase in BMI, there was a change in methylation by 0.0009 for both genes and that for every unit increase in WC, there was a change in methylation by 0.0004. [ 48 ]  According to another story, MSI2 methylation can be a predictor of BMI, accounting 24% of variance. [ 49 ]


Lastly, in a study conducted in 2018, the gene SOCS3, a cytokine signaling suppressor, was found to be upregulated in obesity and was shown to induce leptin and insulin resistance. The paper states "increased SOCS3 expression in obese individuals is associated with several metabolic disorders, including reduced energy expenditure, increased food intake and adiposity, and insulin and leptin resistance. In addition, recent studies found that SOCS3 expression regulates energy and glucose homeostasis in several metabolic conditions, such as pregnancy, caloric restriction, and refeeding". [ 50 ]


To conclude, it cannot be said that physical exercise itself is causing epigenetic changes to reverse obesity. However, it’s been made clear that physical exercise is implicated in certain factors (BMI, metabolic rate, waist circumference) that are the parameters for diagnosing obesity. These parameters themselves are shown to be correlated with epigenetic changes, whether causative or as a symptom.


An increasing amount of evidence shows that physical exercise is also involved in the potential treatment and prevention of neurodegenerative diseases. [ 51 ]  A key assessment thus far is that physical exercise is a key factor for increasing hippocampal adult neurogenesis. [ 52 ]  Physical exercise has also shown to reduce the excessive neuroinflammation generally regarded as the root cause of many neurodegenerative disorders. [ 53 ] [ 54 ]


Studies have found that physical exercise is a viable, non-pharmaceutical approach to resisting and even undoing the harmful processes that cause sudden abnormal changes in brain cell activity resulting in seizures that characterize epilepsy. [ 55 ]  One area of focus looks to the effect on brain-derived neurotrophic factor ( BDNF ) levels following a seizure event. Proper regulation of BDNF levels is necessary to maintain the BDNF-TrkB signaling pathway responsible for healthy synaptic plasticity. [ 56 ]  It has been observed that seizure events are consistently followed by a significant increase then drastic drop in BDNF levels which results in reduced cognition and further increases the probability of seizure events in the future. [ 55 ]  However, animal models have shown that epileptic patients undergoing physical exercise, especially if it's routine, develop more consistent BDNF levels similar to those unafflicted by the disorder. [ 55 ]  This return to normal-like BDNF fluctuations not only promotes generally healthier brain functioning but also reduced the total number of seizures experienced by the treated patients. [ 55 ]  Physical exercise increases BDNF levels via increased H3 acetylation and decreased expression of some relevant histone deacetylases. [ 55 ]  Some evidence has shown that physical exercise also has an impact on the expression of microRNAs related to neurodegeneration. [ 55 ]  The effects of microRNAs are thoroughly discussed above in the effects on cognition section. However, the mechanisms behind exercise and microRNA expression are not clear. Further study is required to understand how significant the interaction is between exercise and microRNA expression. One of the key functions of BDNF is to inhibit reactive oxygen species(ROS) which have been seen to damage cells and consequently discourage proper brain functioning. Physical exercise patients undergoing a high-intensity workout showed a notable increase in ROS that could significantly counter the benefits of moderate BDNF levels discussed prior. [ 55 ]  This finding suggests that low to moderate intensities are preferred treatment methods for those already at risk for neurological dysregulation. [ 55 ]  However, the detrimental effects of high intensity of workouts significantly diminish over time as the person naturally adapts to the oxidative stress that promotes ROS. [ 55 ]


As mentioned previously, neurogenesis impairment is both an indicator and result of neurodegenerative diseases including epilepsy. Studies have shown that subjects manipulated to experience chronic epilepsy showed a significant reduction of granule cells in the dentate gyrus, a subsection of the hippocampus critical to neurogenesis. [ 52 ]  Those same studies then demonstrated how subjects treated with physical exercise showed a return to normal-like granule cell count consequently improving neurogenesis and brain functioning.


Physical exercise has demonstrated to have positive effects on the epigenetic modulation of BDNF levels and neurogenesis maintenance specifically in epileptic patients. [ 55 ]


Alzheimer's disease(AD) is characterized by significant decline in cognition and memory with evidence showing that physical exercise can slow its progression and even provide return of loss function(s) in some cases. [ 57 ]  One of the primary modes of AD is the loss or atypical functionality of microglia and astrocytes caused by excessive build-up of amyloid beta peptide plaque upon the brain. [ 57 ]  The amyloid beta plaque causes the microglia and astrocytes regulatory components to be improperly activated resulting in excessive and inaccurate immune response that targets healthy neurons. [ 57 ]  This interaction acts as a negative feedback loop that creates an environment prone to gross accumulation of amyloid beta plaque. Excessive amounts of amyloid beta plaque triggers improper regulatory mechanisms leading to further neuronal loss and decline in function. Studies have shown, in animal models and human patients alike, that consistent exercise inhibited the improper  microglial activation  mentioned previously through the production of certain myokines. [ 57 ]  Muscle cells respond to contractions by releasing molecules called myokines, one of which is critical to regulating microglial response, IL-6. [ 53 ]  This myokine is produced in response to consistent exercise and has direct influence on the up or down regulation of the inflammatory response involved in neuronal loss depending on signaling pathways. [ 53 ]  Also, IL-6 provokes the production of a cytokine known as IL-10 which can prevent the activation of microglia by blocking its receptors, effectively inhibiting harmful microglial activation mentioned prior. [ 53 ]  A number of patients afflicted by neurodegenerative diseases like AD have notably lower counts of IL-6 which could explain higher instances of dysfunctional inflammatory response. [ 54 ]  Although IL-6 can be artificially induced, long-term exercise is a non-pharmaceutical approach capable of producing IL-6 levels sufficient for normal regulatory processes. [ 53 ]


Similar to epilepsy, exercise has increased BDNF levels in AD patients that were previously lacking. [ 57 ]  Physical exercise increases BDNF levels by increasing H3 acetylation and decreasing some relevant histone deacetylases. [ 55 ]  Brain-derived neurotrophic factor significantly reduces the neuroinflammation strongly associated with Alzheimer's disease and other disorders. [ 57 ]


Physical exercise can play a critical role in regulating inflammatory pathways through the epigenetic modulation of myokine IL-6 and BDNF in AD patients. [ 57 ]


Schizophrenia is characterized by hallucinations, delusions, paranoia, and mood disorder symptoms with evidence showing that physical exercise can alleviate neuroinflammation that could be a root cause of this affective disorder. [ 58 ]  Although it is still uncertain what exactly causes this disorder, several explanations exist such as the dopaminergic and glutamatergic hypotheses. The dopaminergic hypothesis states that schizophrenia is caused by presynaptic dopamine dysregulation. This dysregulation stems from an abnormal increase in key dopamine receptors that results in its excessive release. [ 58 ] [ 59 ]  The glutamatergic hypothesis was previously believed to be closely tied to excessive dopamine release mentioned. [ 58 ]  However, recent literature finds that the dysfunction of N-methyl-D-aspartate receptors(NMDAR) can serve as the mechanism behind schizophrenia. [ 60 ]  Dysfunction of NMDAR receptors causes increased levels of glutamate at non-NMDA sites. Higher generalized glutamate levels in the prefrontal cortex results in atypically high signaling at AMPA receptors. Abnormal signaling activity at the AMPA receptors disrupts cell excitability believed to be connected to schizophrenia. [ 60 ]  A relatively new explanation within the topic focuses on dysfunctional neuroinflammation pathways and oxidative stress similar to what has been discussed in disorders such as Alzheimer's disease. [ 57 ] [ 58 ]  Patients afflicted with schizophrenia show a drastic increase in microglial activation and arachidonic acid signaling, both major inflammation contributors which are known to cause neuronal loss and reduced function. [ 53 ] [ 58 ]  This combination of factors is particularly unique to Schizophrenia patients, so much so that a profile capable of identifying the extent of related inflammation by-products(cytokines and chemokines) is used to diagnose schizophrenia with approximately 90% accuracy. [ 58 ]  As discussed previously, consistent exercise produces greater amounts of myokine IL-6 which regulates inflammatory pathways and increases production of IL-10, a cytokine that inhibits microglial activation. [ 53 ]


One of the primary characteristics of schizophrenia is the occurrence of acute psychosis incited by a range of stressful events depending on an individual's predisposition to stress response. [ 61 ]  An individual's stress response is in large part governed by the hypothalamic-pituitary-adrenal axis or HPA. [ 61 ]  The HPA is multistep biochemical process that results in the release of cortisol from the adrenal gland and consequently excessive dopamine release associated with psychosis. [ 61 ]  Those prone to affected disorders such as schizophrenia are believed to have inherently hyper-active HPA which makes them especially sensitive to stressors. [ 61 ]  Some studies have shown that moderate, long-term exercise has reduced psychotic symptoms by decreasing basal cortisol levels in patients. [ 61 ] [ 62 ]  However, acute, short-term exercise has shown to cause an immediate increase cortisol levels due to the stressful nature of the activity. [ 62 ]  The key point being that consistent exercise over a substantial period of time results in a significantly lower baseline cortisol levels despite the short-term spikes caused by performing the activity. [ 62 ]  Generally lower cortisol levels reduces heightened dopamine release common in patients and brings cortisol levels closer to that of healthy control subjects. [ 61 ]  Although this is by no means a cure, it can notably improve the lives of those affected by mitigating symptoms and normalizing patient response to commons stressors.


Recent studies suggest that schizophrenia patients can benefit from long-term exercise which causes decreased neuroinflammation and basal cortisol levels associated with psychotic events. [ 58 ] [ 62 ]  The epigenetic modulation of basal cortisol levels in schizophrenic patients is just one of several alterations related to this disorder.


The  epigenetics of plant growth and development  refers to the  heritable  changes in  gene expression  that occur without alterations to the DNA sequence, influencing processes in plants such as  seed germination ,  flowering , and  stress responses  through mechanisms like  DNA methylation ,  histone modification , and  chromatin remodeling .


Plants  depend on  epigenetic processes  (mechanisms that regulate gene activity and expression without changing the underlying DNA sequence) for proper function. [ 1 ]  The area of study examines protein interactions with DNA and its associated components, including  histones  and various other modifications such as  methylation , which alter the rate or target of  transcription . Epi-alleles and epi-mutants, much like their genetic counterparts, describe changes in phenotypes due to epigenetic mechanisms. Epigenetics in plants has attracted scientific enthusiasm because of its importance in agriculture.


In the past, macroscopic observations on plants led to a basic understanding of how plants respond to their environments and grow. While these investigations could somewhat correlate cause and effect as a plant develops, they could not truly explain the mechanisms at work without inspection at the molecular level.


Certain studies provided simplistic models with the groundwork for further exploration and eventual explanation through  epigenetics . In 1918,  Gustav Gassner  published findings that noted the necessity of a cold phase for proper plant growth. [ 2 ]  Meanwhile,  Garner  and  Allard  examined the importance of the duration of light exposure to plant growth in 1920. [ 3 ]  Gassner's work would shape the conceptualization of vernalization, which involves epigenetic changes in plants after a period of cold that leads to the development of flowering. [ 4 ]  In a similar manner, Garner and Allard's efforts would gather an awareness of  photoperiodism  which involves epigenetic modifications following the duration of nighttime which enable flowering. [ 5 ]  Rudimentary comprehensions set precedent for later molecular evaluation and, eventually, a more complete view of how plants operate.


Modern epigenetic work depends heavily on bioinformatics to gather large quantities of data relating the function of elements such as intensive looks at DNA sequences or patterns in DNA modifications. With improved methods, flowering mechanisms including vernalization and photoperiodism, Flowering Wageningen, and the underlying processes controlling  germination ,  meristematic tissue , and  heterosis  have been explained through epigenetics.


Research on plants looks at several species. These species are apparently selected on the basis of either conventional model organisms status, such as  Arabidopsis  with its manageability in lab and a known genome, or relevance in agronomy, such as rice, barley or tomatoes.


Epigenetic modifications regulate  gene expression . The transcription of DNA into RNA and subsequent translation into proteins determines the form and function of all living things. The level of DNA transcription generally depends on how accessible DNA is to  transcription factors . Many epigenetic changes occur either on histones, which are normally associated with DNA in  chromatin , or directly on the DNA. For instance,  methylation of DNA  leads to  transcriptional silencing  by denying access to transcription factors.  Histone methylation  can lead to either silencing or activation as determined by the  amino acid  marked. Meanwhile,  histone acetylation  typically lessens the hold of histones on DNA by reducing positive charge, resulting in facilitation of transcription. [ 6 ]


Polycomb group (PcG) proteins and trithorax groups (TrxG) proteins act as key regulators of gene expression through histone  lysine  methylation. PcG proteins repress target genes via Histone 3 lysine 27 trimethylation ( H3K27me3 ), whereas TrxG proteins activate gene expression via histone 3 lysine 4 trimethylation (H3K4me3). [ 7 ]


Long non-coding RNA  can associate with DNA in tandem with proteins to alter the rate of gene expression. These RNA are upwards of 200 base pairs. They can be transcribed from a standalone sequence or be part of a promoter, intron or other component of DNA. Long non-coding RNA often complement functional regions of DNA with overlaps or  antisense . [ 8 ]  To direct transcriptional silencing, a non-coding RNA will associate with a polycomb group protein which to tether it to a specific gene for silencing. [ 7 ]


Germination is the early growth of a plant from a seed. Meanwhile, dormancy precedes germination and serves to preserve a seed until conditions are receptive towards growth. The transition from dormancy to germination seems to depend on the removal of factors inhibiting growth. There are many models for germination which may differ between species. The activity of genes such as Delay of Germination and presence of hormones such as  gibberelins  have been implicated in dormancy while the exact mechanisms surrounding their action is unknown. [ 9 ]


There are at least eighteen  histone deacetylases  in  Arabidopsis . [ 10 ]  Genome-wide association mapping has shown that deacetylation of histones by Histone Deacetylase 2B negatively affects dormancy. The remodeling of chromatin by histone deacetylase leads to silencing of genes that control plant hormones such as  ethylene ,  abscisic acid , and gibberelin which maintain dormancy. Additionally, Histone Deacetylase A6 and A19 activity contributes to silencing of  Cytochrome P450  707A and activation of  9-cis-epoxycarotenoid dioxygenase . Both of these actions lead to increased abscisic acid. [ 9 ]


Methylation by the  methyltransferase  KRYPTONITE causes histone H3 lysine 9 dimethylation which recruits the DNA methyltransferase CHROMOMETHTLASE3 in tandem with HETEROCHROMATIN PROTEIN1. This association methylates cytosine for a stable silencing of Delay of Germination 1 and ABA Insensitive Genes which both contribute to dormancy. [ 9 ]


Flowering is a pivotal step in plant development. Numerous epigenetic factors contribute to the regulation of flowering genes, known as flowering loci (FL). In  Arabidopsis , flowering locus t is responsible for the production of  florigen , which induces Turck_2008 in the shoot apical meristem, a special set of growth tissues, to establish flowering. [ 11 ]  Homologs of the flowering genes exist in flowering plants, but the exact nature of how the genes respond to each mechanism might differ between species. [ 5 ]


Vernalization  depends on the presence of a long non-coding RNA that is termed COLDAIR. The exposure of plants to a significant period of cold results in COLDAIR accumulation. COLDAIR targets  polycomb repressive complex 2  which acts to silence flowering locus C through methylation. [ 4 ]  As flowering locus C is repressed it no longer acts to inhibit the transcription of flowering locus t and SOC1. Flowering locus t and SOC1 activity leads to the development of flowers. [ 12 ]


Another set of flowering controls stems from photoperiodism which initiates flowering based on the length of nighttime. Long day plants flower with a short night, while short day plants require uninterrupted darkness. Some plants are restricted to either condition, while others can operate under a combination of the two, and some plants do not operate under photoperiodism.  In  Arabidopsis , the gene CONSTANS responds to long day conditions and enables flowering when it stops repressing flowering locus t. [ 13 ]  In rice, photoperiodic response is slightly more complex and is controlled by the  florigen  genes Rice Flowering locus T 1 (RFT1) and Heading date 3 a (Hd3a). Hd3a, is a homolog of flowering locus t and, when no longer repressed, activates flowering by directing modification of DNA at the shoot apical meristem with florigen. Heading date 1 (Hd1) is a gene that promotes flowering under short day conditions but represses flowering under long day as it either activates or suppresses Hd3a. Meanwhile, RFT1 can cause flowering under non-inductive long day. Polycomb Repressive Complex 2 can lead to silencing of the genes through histone H3 lysine 27 trimethylation. A variety of chromatin modifications operating in both long and short days or only under one condition can also affect the two florigen genes in rice. [ 5 ]


The gene FWA has been identified as responsible for late flowering in epi-mutants. Epi-mutants are individuals with particular epigenetic changes that lead to a distinct phenotype. As such, both wild type and epi-mutant variants contain identical sequences for FWA. Loss of methylation in direct repeats in the 5' region of the gene results in expression of FWA and subsequent prevention of proper flowering. The gene is normally silenced by methylation of DNA in tissues not related to flowering (Soppe et al. 2000). [ 14 ]


Meristematic tissues contain cells that continue to grow and differentiate throughout the plant's lifetime. Shoot apical meristem gives rise to flowers and leaves while root apical meristem grows into roots. These components are crucial to general plant growth and are the harbingers of development. Meristematic tissue apparently contains characteristic epigenetic modifications. For example, the boundary between the proximal meristem and elongation zone showed elevated  H4K5ac  along with a high level of 5mC in barley. Root meristematic tissues have been found to contain patterns for histone H4 lysine 5 acetylation, histone H3 lysine 4 and 9 di methylation and DNA methylation as 5-methyl cytosine. So far, only a causal correlation between epigenetic marks and tissue types has been established and further study is required to understand the exact involvement of the marks. [ 15 ]


Heterosis is defined as any advantages seen in hybrids. The effects of heterosis seem to follow a rather simple epigenetic premise in plants. In hybrids, lack of proper regulatory action, such as silencing by methylation, leads to uninhibited genes. If the gene is involved in growth, such as photosynthesis, the plant will experience increased vitality. [ 16 ]


The results heterosis can be seen in traits such as increased fruit yield, earlier ripening, and heat tolerance. Heterosis has been shown to provide increased general growth and fruit yield in tomato plants. [ 17 ]


The  epigenetics of schizophrenia  is the study of how inherited  epigenetic  changes are regulated and modified by the environment and external factors and how these changes influence the onset and development of, and vulnerability to,  schizophrenia . Epigenetics concerns the heritability of those changes, too. Schizophrenia is a debilitating and often misunderstood disorder that affects up to 1% of the world's population. [ 1 ]  Although schizophrenia is a heavily studied disorder, it has remained largely impervious to scientific understanding; epigenetics offers a new avenue for research, understanding, and treatment.


Historically, schizophrenia has been studied and examined through different paradigms, or schools of thought. In the late 1870s,  Emil Kraepelin  started the idea of studying it as an illness. Another paradigm, introduced by Zubin and Spring in 1977, was the  stress-vulnerability model  where the individual has unique characteristics that give him or her strengths or vulnerabilities to deal with stress, a predisposition for schizophrenia. More recently, with the decoding of the human genome, there had been a focus on identifying specific genes to study the disease. However, the genetics paradigm faced problems with inconsistent, inconclusive, and variable results. The most recent school of thought is studying schizophrenia through epigenetics. [ 2 ]


The idea of epigenetics has been described as far back as 1942, when Conrad Waddington described it as how the environment regulated genetics. As the field and available technology has progressed, the term has come to also refer to the molecular mechanisms of regulation. The concept that these epigenetic changes can be passed on to future generations has progressively become more accepted. [ 3 ]


While epigenetics is a relatively new field of study, specific applications and focus on mental disorders like schizophrenia is an even more recent area of research.


The core symptoms of schizophrenia can be classified into three broad categories. These symptoms are often used to build and study  animal models of schizophrenia  in the field of epigenetics. [ 1 ]  Positive symptoms are considered  limbic  system aberrations, while negative and cognitive symptoms are thought of as frontal lobe abnormalities. [ 4 ]


Positive symptoms:


Negative Symptoms:


Cognitive dysfunctions:


Heritability represents the percentage in variability in a trait that comes from genetic differences. There is a great deal of evidence to show that schizophrenia is a heritable disease. It has been calculated that the heritability of  schizophrenia is around 80%, and within that heritability 30% of the variability comes from single nucleotide polymorphisms and another 30% from large  copy number variants  (CNVs). One key piece of evidence is a twin study that showed that the likelihood of developing the disease is 53% for one member of monozygotic twins (twins with same genetic code), compared to the 15% for dizygotic twins, who don't share the exact DNA. [ 5 ]  It has also been shown that having direct family members that are diagnosed with schizophrenia increases the rate of developing schizophrenia by 9 times. Another study investigated the rates of schizophrenia of adoptees: adoptees with a genetic history of schizophrenia that were adopted by non-schizophrenic parents were seen to be diagnosed with schizophrenia at higher rates than adoptees without a biological history of schizophrenia but raised with adoptive parents diagnosed with schizophrenia. [ 1 ]  However, the extent to which interactions between environmental and genetic factors contribute to the development of schizophrenia is uncertain. Others question the evidence of heritability due to different definitions of schizophrenia and the similar environment for both twins. [ 6 ] [ 7 ]  That said, the fact that even monozygotic twins don't share a 100%  concordance  rate suggests environmental factors play a role in the vulnerability and development of the disorder.


Maternal immune responses are involved in schizophrenia development. A 2019 study found that, in mice models, maternal immune activation may be involved in the regulation of the ARX gene expression that contributes to the GABA dysfunction commonly implicated in schizophrenia. [ 8 ]  Most maternal effects involved in schizophrenia development have to do with immune system activation and associated cytokine and neurogenesis mechanisms rather than genetic changes.


Paternal genetic effects are seen to be involved in the rate of development of schizophrenia. A 2021 study showed that advanced paternal age was associated with higher schizophrenia risk. In the study, the paternal ages were grouped into 5-year increments, and it was seen that as the increments increased, so did the risk of developing schizophrenia. [ 9 ]  It is hypothesized that advanced paternal age increases schizophrenia risk because fathers pass down three to four times more de novo mutations than do mothers. [ 10 ]  It is estimated that 2 new de novo mutations are created a year, resulting in fathers with an advanced age passing down more mutations to their offspring, which may explain the increased rates of schizophrenia . [ 10 ]


There are various environmental factors that have been suggested, including the use of marijuana, complications during pregnancy, socioeconomic status and environment, and maternal malnutrition. In some circumstances, it has been shown that environmental factors can increase the risk of schizophrenia when combined with a family history of psychosis. [ 11 ]  As the field of epigenetics advances, these and other external risk factors are likely to be considered in epidemiological studies. [ 1 ]


Among the many genes known to be associated with schizophrenia, a few have been identified as particularly important when studying the epigenetic phenomena underlying the disease.


Both proteins are expressed by GABAergic neurons. Several studies have demonstrated that levels of both reelin and GAD67 are downregulated in patients with schizophrenia and animal models.


Genome-wide association studies  (GWAS) have confirmed the presence of other genes thought to be involved in the regulation of schizophrenia. [ 11 ]  Several genes that GWAS have determined to be associated with schizophrenia include genes involved in neurodevelopment, including glutamatergic signaling, synaptic transmission, and the regulation of voltage-gated calcium channels. [ 13 ]  This includes the GAD1 and RELN pathways denoted above as well as BDNF. Another important  gene is the Dopamine Receptor 2 gene, which encodes a dopamine receptor (D2), a primary target of many of the antipsychotic drugs that are used to treat patients with schizophrenia. [ 13 ] [ 14 ]  Chromosomal regions containing a large number of CNVs are reported to lead to increased susceptibility to schizophrenia. [ 11 ]


Copy number variants  (CNVs) have also been reported to be associated with schizophrenia, particularly in chromosomal regions with large amounts of CNVs. [ 13 ] [ 11 ]  A CNV located at the gene NRXN1, which encodes a neurexin protein involved in synaptic transmission, is thought to cause a loss-of-function mutation that is associated with the development of schizophrenia. [ 13 ]  Loss-of-function mutations at the gene encoding histone H3 methyltransferase, an important enzyme for epigenetic histone modification, have also been implicated in gene-association studies for schizophrenia. [ 13 ]  Histone modification is not the only epigenetic mechanism thought to be commonly associated with schizophrenia. Analyzing schizophrenia-associated genes reveals that risk loci are commonly found near DNA methylation quantitative trait loci (which affect CpG methylation), which have post-transcriptional modifications uniquely correlated to schizophrenia and produce splice variants with strong chromatin associations. [ 13 ]  DNA methylation, post-transcriptional modification and splice variation, and chromatin modifications are all prominent epigenetic mechanisms, and their association with schizophrenia-risk-associated loci indicates that these mechanisms may play a significant role in the development of the disease.


Moving away from GWAS,  linkage studies  have proved to be unsuccessful due to the interaction of several different genes that are all involved in the development of schizophrenia. [ 11 ]  There are also few specific SNPs majorly involved in the development of schizophrenia, however groups of SNPs could account for 30% of the genetic susceptibility for developing schizophrenia. [ 13 ] [ 11 ]


Epigenetics can be studied and researched through various methods. One of the most common methods is looking at  postmortem brain tissue  of patients with schizophrenia and analyzing them for biomarkers. Other common methods include tissue culture studies of neurons, genome-wide analysis of non-brain cells in living patients (see  PBMC ), and transgenic and schizophrenic animal models. [ 1 ]


Other studies that are currently being done or that can be done in the future include longitudinal studies of patients, "at-risk" populations, and monozygotic twins, and studies that  examine specific gene-environment interactions and epigenetic effects. [ 15 ]


Epigenetics (translated as "above genetics") is the study of how genes are regulated through reversible and heritable molecular mechanisms. The epigenetic changes modify gene expression through either activation of the gene that codes for a certain protein, or repression of the gene. There are two main categories of modifications: the  methylation  of  DNA  and modifications to  histones . Research findings have demonstrated that several examples of both of these changes are linked to schizophrenia and its symptoms. [ 13 ] [ 1 ]  Evidence of epigenetic regulation is still sparse, and just as genetic culprits for the disease remain nebulous, there is no definite answer to what epigenetic alterations should be expected in patients with schizophrenia.


DNA methylation is the covalent addition of a  methyl  group to a segment of the DNA code. These -CH3 groups are added to  cytosine  residues by the  DNMT  (DNA Methytransferases) enzymes. The binding methyl group to  promoter  regions interferes with the binding of  transcription factors  and silences the gene by preventing the transcription of that code. [ 1 ]  DNA methylation is one of the most well studied epigenetic mechanisms and there have been several findings linking it to schizophrenia.


Differential  DNA methylation  has been identified in the schizophrenic epigenome across 4 different regions of the brain. [ 13 ]  Hypermethylation of genes in neurotransmitter pathways (including GAD1, RELN, and the serotonin pathway) as well as hypomethylation of genes in other pathways (such as the dopaminergic pathway) have been observed in schizophrenic patients. [ 14 ] [ 13 ]  A broad range of genomic methylation patterns have been observed in patients with schizophrenia, and although a definite explanation is not in place, there are enough consistent abnormalities to suspect that differential methylation may play a substantial role in the pathogenesis of schizophrenia.


It has been consistently shown in various studies that levels of reelin and GAD67 are downregulated in the cortical and  hippocampal  tissue samples of individuals with schizophrenia. These proteins are used by GABAergic neurons, and abnormalities in their levels could result in some of the symptoms found in individuals with schizophrenia. The genes for these two proteins are found in areas of the genetic code that can be methylated (see  CpG island ).
Recent studies have demonstrated an epigenetic link between the levels of the proteins and schizophrenia. One study found that cortical neurons with lower levels of GAD67 and reelin also showed increased levels of DNMT1, one of the enzymes that adds a methyl group. It has also been shown that a schizophrenic-type state can be induced in mice when they were chronically given l-methionine, a precursor necessary for DNMT activity. These and other findings provide a strong link between epigenetic changes and schizophrenia. [ 12 ]


DNA methylation can also affect expression of BDNF (brain derived neurotrophic factor). The BDNF protein is important for cognition, learning, and even vulnerability to early life trauma. Sun et al. showed that fear condition led to changes in DNA methylation levels in BDNF promoter regions in hippocampal neurons. It was also shown that inhibiting DNMT activity led to change in levels of BDNF in the hippocampus. Methylation of BDNF DNA has also been shown to be affected by post-natal social experiences, stressful environment, and social interaction deprivation. Furthermore, these stimuli have also been linked to increased anxiety, problems with cognition, etc. While a direct link between schizophrenia and BDNF levels hasn't been established, these findings suggest a relation to many problems that are similar to symptoms. [ 1 ]


Histones are proteins that the DNA chromosome are wrapped around. Histones are present as an octamer (set of 8 proteins) and they can be modified through  acetylation ,  methylation ,  SUMOylation ,  ubiquitination ,  phosphorylation , etc. These changes can either open or close up the chromosome. Thus, depending on which histone is modified and the exact process, histone modifications can either silence or promote gene expression (while DNA methylation almost always silences).


Because the sub-field of histone modifications is relatively new, there aren't many results yet. Investigations into these epigenetic regulations indicate that therapeutic pathways targeting epigenetic mechanisms like differential methylation and acetylation may be beneficial. [ 13 ]  Some studies have found that patients with schizophrenia have higher levels of methylation at H3 (the 3rd histone in the octamer) in the prefrontal cortex, an area that could be related to the negative symptoms. A prominent example is the increased repressive methylation of histone 3 (H3K9me2), which has been associated with both age of disease onset and treatment resistance. [ 13 ]   It has also been shown that histone acetylation and  phosphorylation  is increased at the promoter for the BDNF protein, which is involved in learning and memory. [ 1 ]


More recent studies have found that postmortem brain tissue from patients with schizophrenia had higher levels of  HDAC , histone deacetylase, an enzyme that remove acetyl groups from histones. HDAC1 levels are inversely correlated with GAD67 protein expression, which is decreased in patients with schizophrenia. [ 12 ]


Studies have shown that epigenetic changes can be passed on to future generations through meiosis and mitosis. [ 16 ]  These findings suggest that environmental factors that the parents face can possibly affect how the child's genetic code is regulated. Research findings have shown this to be true for patients with schizophrenia as well. In rats, the transmission of maternal behavior and even stress responses can be attributed to how certain genes in the hippocampus of the mother are methylated. [ 1 ]  Another study has shown that the methylation of the BDNF gene, which can be affected by early life stress and abuse, is also transmittable to future generations. [ 17 ]


In addition to epigenetic effects as a result of maternal influence during important stages of neurodevelopment, studies show that nutrient deprivation can result in epigenetic modifications that are maintained from generation to generation. [ 13 ]  Historically, famines are thought to cause changes in epigenetic regulation within the human genome. [ 13 ]  Specifically, deprivation of nutrients is thought to alter methylation patterns in mammals, and several case studies have shown that periods of famine are positively correlated to increased incidences of schizophrenia in certain populations. [ 13 ]  Babies born during periods of famine were up to twice as likely to develop schizophrenia or schizophrenia spectrum disorder. [ 18 ] [ 19 ]  Thus, researchers believe that the development of schizophrenia is linked to nutrient deprivation. The leading hypothesis for how this is accomplished is via subtle epigenetic alterations following nutrient deprivation, such as the hypermethylation of genes in neurotransmitter pathways, since it is well documented that dietary restriction has an effect on DNA methylation states. [ 13 ]  This line of thinking is further supported by studies showing that deficiencies in certain nutrients, including choline, folate and vitamin B12 which are required for the creation  S-adenosylmethionine  (SAM), are also linked with increasing the epigenetic factors associated with increased  risk of schizophrenia. [ 11 ]  Evidence is still mounting in this area, but the existing correlations are notably strong.


While there haven't been many studies linking environmental factors to schizophrenia-related epigenetics mechanisms at this point in the field, a few studies have shown interesting results.
Advanced paternal age is one of the risk factors for schizophrenia, according to recent research. This is  through mutagenesis, which cause further spontaneous changes, or through genomic imprinting. As the parent ages, more and more errors may occur in the epigenetic process. [ 20 ]  There is also evidence of the association between the inhalation of benzene through the burning of wood and schizophrenic development. This might occur through epigenetic changes. [ 21 ]  Methamphetamine has also been linked to schizophrenia or similar psychotic symptoms. A recent study found that methamphetamine users had altered DNMT1 levels, similar to how patients with schizophrenia have shown abnormal levels of DNMT1 in GABAergic neurons. [ 22 ]


Research has shown that there is not a 100% likelihood for genetically inheriting schizophrenia- as in monozygotic twin pairs, when one twin is diagnosed with schizophrenia, there is only a 50% chance that the other twin will also be diagnosed with schizophrenia. This finding shows that environmental influences play a role in the development of schizophrenia. [ 1 ]


Maternal effects  have also been shown to increase the rate of schizophrenia. It has been hypothesized that babies born in winter and spring have higher rates of schizophrenia than babies born in the summer and fall because of the increase in respiratory infections during the colder months. Furthermore, a study showed that maternal respiratory infection increased the rate of schizophrenia "three- to sevenfold," and if the mothers would not have gotten the respiratory infection, "14 to 21% of schizophrenia cases would have been prevented." The relative amounts of pro-inflammatory and anti-inflammatory compounds found in maternal serum are associated with the onset of schizophrenia, as seen in studies in which amounts of interleukin 6 and interleukin 10, pro- and anti- inflammatory, respectively, were manipulated. It was reported that increasing the amount of interleukin 10 or decreasing the amount of interleukin 6 lessened the effects of the immune system on the fetus. [ 23 ]  These long-lasting impacts may indicate an epigenetic effects in the offspring, however, it remains unconfirmed. A 2018 study found that patients with schizophrenia had hypomethylation—associated with increased expression of a gene—of the IP6 promoter region compared to the control subjects. [ 24 ]


DNA methylation patterns have been linked with increased schizophrenia risk. Specifically, the hypermethylation of the promoter region has been reported to suppress expression of  reelin  (RELN) in the frontal and prefrontal cortex. Higher DNA methylation levels of RELN promoters has been observed in schizophrenic patients. [ 25 ]  Several other genes, including GABAergic, dopaminergic, and serotonergic genes, have also been found to have different methylation in patterns in those affected by schizophrenia. Those with schizophrenia have also been noted to have increased amounts of DNMT1, which is involved in the regulation of methylation at CpG sites. Jaffe et al. recently found that 2104 CpG sites were differently methylated in the prefrontal cortex those with schizophrenia as compared to those without schizophrenia. Most notably, the differentially methylated sites were found in genes having to do with "embryonic development, cell fate commitment, and nervous system differentiation" as well as the time period between late gestation and early life. [ 26 ]


Prenatal Maternal Stress  (PNMS) is also associated with schizophrenia and schizophrenia spectrum disorders (SSD). Several studies have shown that increased PNMS is linked to decreased fetal growth in males who later develop SSD. It has also been found that PNMS leading to increased morbidity and mortality outcomes are also associates with increased risk of SSD development in males. PNMS, especially in early pregnancy, has also been associated to motor deficiencies and behavioral difficulties in the pre-morbid period before schizophrenia onset, most notably in males. [ 27 ]


One of the most interesting findings relating an environmental factor with schizophrenic epigenetic mechanisms is exposure to nicotine. It has been widely reported that 80% of patients with schizophrenia use some form of tobacco. [ 28 ]  Furthermore, smoking appeared to increase cognition in individuals with schizophrenia. However, it was only a recent study Satta et al.that showed that nicotine leads to decreased levels of DNMT1 in GABAergic mouse neurons, a molecule which adds methyl groups to DNA. This led to increased expression of GAD67. [ 29 ]


There are several limitations to current research methods and scientific findings. One problem with postmortem studies is that they only demonstrate a single snapshot of a patient with schizophrenia. Thus, it is hard to relate whether biomarker findings are related to the pathology of schizophrenia.


Another limitation is that the most relevant tissue, that of the brain, is impossible to obtain in living, patients with schizophrenia. To work around this, several studies have used more accessible sources, like lymphocytes or germ cell lines, since some studies have shown that epigenetic mutations can be detected in other tissues.


Epigenetic studies of disorders like schizophrenia are also subject to the subjectivity of psychiatric diagnoses and the spectrum-like nature of mental health problems. This problem with classification of mental health problems have led to intermediate phenotypes that might be better fit. [ 15 ]


The advent of epigenetics as an avenue to pursue schizophrenic research has brought about many possibilities for both early detection, diagnoses, and treatment.  While this field is still at an early stage, there have already been promising findings. Some postmortem brain studies looking at the gene expression of histone methylation has shown promising results that might be used for early detection in other patients. However, the bulk of the translational research focus and findings have been on therapeutic interventions. [ 12 ]


Since epigenetic changes are reversible and susceptible pharmacological treatments and drugs, there is a great deal of promise in developing treatments. As many have pointed out, schizophrenia is a lifelong disorder that has widespread effects. Thus, it may not be possible to fully reverse the disease. Although irreversible, the lives of patients with schizophrenia can be greatly improved through treatments that alleviate symptoms. Treatments like anti-psychotic medications for schizophrenia are effective, but they often have serious side effects, and medical practitioners are always looking to improve patients' treatment outcomes. Recent studies indicate that it may be possible to improve upon existing treatments through epigenetic means. This provides a promising new direction for disease management. Pharmaceuticals that directly affect epigenetic markers could be used to improve the efficacy of a patient's current treatment or serve as an updated treatment regiment altogether.


As previously discussed, schizophrenia is associated with elevated levels of gene methylation and repressive histone marks, including H3K9me2.  Mood stabilizers  have become a therapeutic method of interest in treating schizophrenia due to their ability to reverse epigenetic alterations like repressive histone marks. [ 30 ]  Mood stabilizers that are known to target epigenetic markers associated with schizophrenia include  lithium ,  valproate ,  lamotrigine , and  carbamazepine . [ 30 ]


HDAC  (histone deacetylase) inhibitors are one class of drugs that are being investigated. Studies have shown that levels of reelin and GAD67 (which are decreased in schizophrenic animal models) are both upregulated after treatment with HDAC inhibitors. Furthermore, there is the added benefit of selectivity, as HDAC inhibitors can be specific to cell type, tissue type, and even regions of the brain. [ 12 ]


Valproate, a psychotropic drug, is an HDAC inhibitor that is frequently used to treat patients with schizophrenia. [ 30 ]  Valproate leads to both increased H3 and H4 acetylation as well as increased GAD67 and reelin mRNA levels in lymphocytes. [ 30 ]   Lithium has also been shown to be highly effective at increasing histone acetylation and presence of GAD67 and reelin transcripts in patients experiencing psychotic symptoms. [ 30 ]


HMT  (histone demethylase) inhibitors also act on histones. They prevent the demethylation of the H3K4 histone protein and open up that part of the chromatin. Tranylcypromine, an  antidepressant , has been shown to have HMT inhibitory properties, and in a study, treatment of patients with schizophrenia with tranylcypromine showed improvements regarding negative symptoms. [ 12 ]


In early studies,  imipramine , an antidepressant drug, was shown to be able to remove the repressive epigenetic mark H3K9me2. [ 13 ]  Decreasing repression at this marker appears to improve treatment outcomes for patients taking antipsychotic medications. [ 31 ] [ 32 ]


Among long-term antipsychotic users, post-mortem tissue analysis finds that genes that are typically methylated in patients with psychosis are hypomethylated after lifelong antipsychotic use. [ 33 ]  In other words, anti-psychotic drugs are able to reduce methylation of genes in long-term users. Removing repressive epigenetic marks is only part of how these drugs modify the epigenome of patients with psychotic symptoms. Antipsychotics are associated with both the induction and inhibition of DNA methylation, which can lead to the simultaneous upregulation and downregulation of different genes in patients. [ 33 ]  While significant variation in methylation patterns have been recorded in patients using antipsychotic drugs, the evidence in this area is not yet sufficient to determine the exact mechanism underlying how these drugs influence methylation. [ 33 ]  Schizophrenia is a complex, multifaceted illness, and the variety of methylation patterns observed affirms this knowledge.


DNMT inhibitors have also been shown to increase levels of the reeling protein and GAD67 in cell cultures. Some of the current DNMT inhibitors, however, like zebularine and procainamide, do not cross the blood brain barrier and would not prove as effective a treatment. While DNMT inhibitors would prevent the addition of a methyl group, there is also research done on DNA demethylate inducers, which would pharmacologically induce the removal of methyl groups. Current antipsychotic drugs, like  clozapine  and  sulpiride , have been shown to also induce demethylation. [ 12 ]


In  biology , the  epigenome  of an organism is the collection of chemical changes to its  DNA  and  histone  proteins that affects when, where, and how the DNA is  expressed ; these changes can be passed down to an organism's offspring via  transgenerational epigenetic inheritance . Changes to the epigenome can result in changes to the structure of  chromatin  and changes to the function of the  genome . [ 1 ]  The  human epigenome , including  DNA methylation  and  histone modification , is maintained through cell division (both  mitosis  and  meiosis ). [ 2 ]  The epigenome is essential for normal  development  and  cellular differentiation , enabling cells with the same genetic code to perform different functions. The human epigenome is dynamic and can be influenced by environmental factors such as  diet ,  stress , and  toxins .


The epigenome is involved in regulating gene expression, development, tissue differentiation, and suppression of  transposable elements . Unlike the underlying genome, which remains largely static within an individual, the epigenome can be dynamically altered by environmental conditions.


The main types of epigenetic changes include: [ 3 ]


Addition of a methyl group to the DNA molecule, typically at  cytosine  bases. This modification generally leads to  gene silencing  by preventing the binding of  transcription factors  and other proteins necessary for gene expression. [ 3 ]


DNA functionally interacts with a variety of epigenetic marks, such as cytosine methylation, also known as  5-methylcytosine  (5mC). This epigenetic mark is widely conserved and plays major roles in the regulation of gene expression, in the silencing of  transposable elements  and  repeat sequences . [ 4 ]


Individuals differ with their epigenetic profile, for example the variance in  CpG  methylation among individuals is about 42%. On the contrary, epigenetic profile (including methylation profile) of each individual is constant over the course of a year, reflecting the constancy of our  phenotype  and metabolic traits. Methylation profile, in particular, is quite stable in a 12-month period and appears to change more over decades. [ 5 ]


CoRSIVs are  Co rrelated  R egions of  S ystemic  I nterindividual  V ariation in DNA methylation. They span only 0.1% of the human genome, so they are very rare; they can be inter-correlated over long genomic distances (>50 kbp). CoRSIVs are also associated with genes involved in a lot of human disorders, including tumors, mental disorders and cardiovascular diseases. It has been observed that disease-associated CpG sites are 37% enriched in CoRSIVs compared to control regions and 53% enriched in CoRSIVs relative to tDMRs (tissue specific Differentially Methylated Regions). [ 6 ]


Most of the CoRSIVs are only 200 – 300 bp long and include 5–10 CpG dinucleotides, the largest span several kb and involve hundreds of CpGs. These regions tend to occur in clusters and the two genomic areas of high CoRSIV density are observed at the major histocompatibility ( MHC ) locus on  chromosome 6  and at the pericentromeric region on the long arm of chromosome 20. [ 6 ]


CoRSIVs are enriched in  intergenic  and quiescent regions (e.g.  subtelomeric  regions) and contain many transposable elements, but few CpG islands (CGI) and transcription factor binding sites. CoRSIVs are under-represented in the proximity of genes, in  heterochromatic  regions, active  promoters , and  enhancers . They are also usually not present in highly conserved genomic regions. [ 6 ]


CoRSIVs can have a useful application: measurements of CoRSIV methylation in one tissue can provide some information about epigenetic regulation in other tissues, indeed we can predict the expression of associated genes because systemic epigenetic variants are generally consistent in all tissues and cell types. [ 7 ]


Quantification of the heritable basis underlying population epigenomic variation is also important to delineate its cis- and trans-regulatory architecture. In particular, most studies state that inter-individual differences in DNA methylation are mainly determined by cis-regulatory sequence  polymorphisms , probably involving mutations in TFBSs (Transcription Factor Binding Sites) with downstream consequences on local chromatin environment. The sparsity of  trans-acting  polymorphisms in humans suggests that such effects are highly deleterious. Indeed, trans-acting factors are expected to be caused by mutations in chromatin control genes or other highly pleiotropic regulators. If trans-acting variants do exist in human populations, they probably segregate as rare alleles or originate from somatic mutations and present with clinical phenotypes, as is the case in many cancers. [ 4 ]


DNA methylation (in particular in CpG regions) is able to affect gene expression: hypermethylated regions tend to be differentially expressed. In fact, people with a similar methylation profile tend to also have the same  transcriptome . Moreover, one key observation from human methylation is that most functionally relevant changes in CpG methylation occur in regulatory elements, such as enhancers.


Anyway, differential expression concerns only a slight number of methylated genes: only one fifth of genes with CpG methylation shows variable expression according to their methylation state. It is important to notice that methylation is not the only factor affecting  gene regulation . [ 5 ]


It was revealed by  immunostaining  experiments that in human preimplantation embryos there is a global DNA  demethylation  process. After  fertilisation , the  DNA methylation  level decreases sharply in the early  pronuclei . This is a consequence of active DNA demethylation at this stage. But global demethylation is not an irreversible process, in fact  de novo  methylation occurring from the early to mid-pronuclear stage and from the 4-cell to the 8-cell stage. [ 8 ]


The percentage of DNA methylation is different in  oocytes  and in  sperm : the mature oocyte has an intermediate level of DNA methylation (72%), instead the sperm has high level of DNA methylation (86%). Demethylation in paternal genome occurs quickly after fertilisation, whereas the maternal genome is quite resistant at the demethylation process at this stage. Maternal different methylated regions (DMRs) are more resistant to the preimplantation demethylation wave. [ 8 ]


CpG methylation is similar in  germinal vesicle  (GV) stage, intermediate  metaphase I  (MI) stage and mature  metaphase II  (MII) stage. Non-CpG methylation continues to accumulate in these stages. [ 8 ]


Chromatin  accessibility in germline was evaluated by different approaches, like sc ATAC-seq  and sciATAC-seq, scCOOL-seq, scNOMe-seq and sc DNase-seq . Stage-specific proximal and distal regions with accessible chromatin regions were identified. Global chromatin accessibility is found to gradually decrease from the  zygote  to the 8-cell stage and then increase. Parental allele-specific analysis shows that paternal genome becomes more open than the maternal genome from the late zygote stage to the 4-cell stage, which may reflect decondensation of the paternal genome with replacement of  protamines  by  histones . [ 8 ]


DNA methylation imbalances between homologous chromosomes show sequence-dependent behavior. Difference in the methylation state of neighboring cytosines on the same chromosome occurs due to the difference in DNA sequence between the chromosomes. Whole-genome  bisulfite sequencing  (WGBS) is used to explore sequence-dependent allele-specific methylation (SD-ASM) at a single-chromosome resolution level and comprehensive whole-genome coverage. The results of WGBS tested on 49 methylomes revealed CpG methylation imbalances exceeding 30% differences in 5% of the loci. [ 9 ]


On the sites of gene regulatory loci bound by transcription factors the random switching between methylated and unmethylated states of DNA was observed. This is also referred as stochastic switching and it is linked to selective buffering of  gene regulatory circuit  against mutations and genetic diseases. Only rare genetic variants show the stochastic type of gene regulation.