Epigenetics across the human lifespan

Aging is a multifactorial process that results in a progressive loss of regenerative capacity through a decline in cell-proliferation and tissue functionality (Campisi, 2013 ). It induces global and complex changes in the human DNA methylation landscape (Xu and Taylor, 2014 ). Additional epigenetic changes have been described which provide clues to understanding the aging process. For example, senescent cells are characterized by formation of a specialized heterochromatin called senescence-associated heterochromatin foci that exhibit noticeable histone modifications (Narita et al., 2003 ). These foci contribute to senescence-associated proliferation arrest that may silence the expression of proliferation-promoting genes (Sedivy et al., 2008 ). Shortened telomeres, a hallmark of aging, may have reduced heterochromatin (Benetti et al., 2007 ). Generally, during the aging process, global hypomethylation of DNA occurs in a repetitive sequence pattern that may promote genomic instability (Heyn et al., 2012 ). Not only is aging correlated with hypomethylation of proto-oncogenes, but also with hypermethylation of tumor suppressor genes, potentially leading to increased risk of cancer and other diseases (Coppede, 2014 ). Some methylation changes are so predictable that age-related DNA methylation patterns have been used to predict an individual's actual chronological age, such that DNA methylation can be used as a measure of age or age acceleration, as so-called “aging clock” (Horvath, 2013 ). Epigenetic changes in disease are not always focal, but can be global and encompass large chromosomal regions. For example the aberrant expression of micro RNAs has been linked to various age-related diseases such as Alzheimer's disease, cardiac disease and many cancers including leukemia and lymphoma (Natarajan et al., 1992 ; Fabbri et al., 2009 ; Cheng and Zhang, 2010 ; Montgomery and Van Rooij, 2010 ; Provost, 2010 ), as described below. Alzheimer's disease is a neurodegenerative disorder characterized by β-Amyloid, inflammatory, oxidative and vascular damage. DNA hypomethylation of the entorhinal region of the cerebral cortex, plus hypermethylation and consequent overexpression of the hTERT gene have been reported in Alzheimer's research (Silva et al., 2008 ; Mastroeni et al., 2010 ). Animal studies suggest that overexpression of histone deacetylase 2 (HDAC 2) may decrease synaptic plasticity and impair memory formation (Guan et al., 2009 ; Urdinguio et al., 2009 ). Also, DNA methylation deficiency can accelerate age-related diseases and it has been shown that Dnmt1 haploinsufficiency can impair learning and memory function causing cognitive disorders with age (Liu et al., 2011 ). The epigenetic basis of osteoarthritis (OA) is seen in the fact that OA chondrocytes express genes involved in degradation of cartilage as a result of their hypomethylated promoters under the influence of cytokines like IL-1β and TNF-α, as opposed to normal chondrocytes (Haseeb et al., 2014 ). Heart disease is often attributed to genetic predisposition, but epigenetic marks that vary between cell types and respond to endogenous and exogenous stimuli likely share culpability (Ordovas and Smith, 2010 ). DNA methylation is critical for the development of atherosclerosis and cardiovascular disease; recently hypermethylation has been shown in differentially methylated genomic regions of patients suffering with coronoary artery disease (CAD) (Sharma et al., 2014 ). DNA methyltransferases ( DNMT s) exhibit hypomethylation in mice, an observation associated with increased expression of inflammatory mediators (Makar and Wilson, 2004 ). Also, DNA hypermethylation has been observed in the estrogen receptor genes ESR1 and ESR2 of vascular smooth muscle which contributes to atherosclerosis (Lund and Zaina, 2011 ). Not only is DNA methylation a primary regulator of inflammation, but also controls leukocyte functions related to cardiovascular risk (Baccarelli et al., 2010 ). Removal of epigenetic signatures of oxidative and inflammatory genes has been proposed as a promising therapeutic option to prevent endothelial dysfunction and vascular complications in diabetic people (Paneni et al., 2013 ). Histone modification has also been implicated in various aspects of cardiovascular disease such as angiogenesis and myocardial infarction (Webster et al., 2013 ). Histones are important for the normal regulation of the NOS3 gene. This gene codes for the protein eNOS that catalyzes formation of NO, a vasodilating factor in blood vessels that operates in the regulation of healthy cardiovascular tissue and can inhibit the ability of KDM3a protein to remove histone methyl groups (Hickok et al., 2013 ). Cancer has long been considered a disease of genetic origin, but an historic link between cancer and epigenetics was identified when DNA of colorectal cancer patients was observed to be hypomethylated (Feinberg and Vogelstein, 1983 ). The normally hypermethylated and silent regions of the genome which contain repetitive sequences become demethylated. Conversely, hypermethylation of CpG islands in certain cancers is correlated with abnormal gene activity, such as deactivation of tumor suppressor genes (Esteller, 2002 ). Hypermethylation of DNA also damages repetitive sequences of DNA called mircosatellites (Oki et al., 1999 ); hypermethylation of the MLH1 promoter (a DNA repair gene) disfigures microsatellites, a phenomenon present in many cancers including colorectal and ovarian (Jones and Baylin, 2002 ). These observations of promoter hypermethylation (Coppede, 2014 ) and heterochromatinization (Rideout et al., 1994 ) are compelling evidence of the dramatic influence of epigenetics on tumorigenesis. A major locus susceptible to transcriptional silencing as a result of promoter hypermethylation is the INK4 locus located on chromosome 9 (Kim and Sharpless, 2006 ). INK4 represents a family of cyclin-dependent kinase inhibitors. This gene encodes several proteins that are often targeted early during malignant progression, including p14, p15, and p16. Histone modification is another epigenetically important mechanism prevalent during carcinogenic transformation. Transcriptional control of p16 is interrupted when chromatin domains are lost and discrete histone structure is destroyed, in breast cancer cells for example (Witcher and Emerson, 2009 ). Epigenetic changes differ from their genetic counterparts such as gene mutations in that epigenetic hypermethylation affects many genes within a single cancer cell (Coppede, 2014 ). For example, PIAS1, a transcriptional repressor, is involved in the progression of breast cancer and operates on an epigenetic level through gene silencing by recruting DNMTs (Liu et al., 2014 ). Still, many researchers view the link between cancer and epigenetics with optimism, since epigenetic modifications are potentially reversible. For example, it is thought that cells harboring gene mutations must be killed or removed to prevent uncontrolled propagation of the damaged code. But advances in epigenetic technology may soon allow repair of defective epigenetic modifications by a variety of therapeutics. For example the drug azacitidine, the first FDA-approved epigenomic drug, treats leukemia by reactivating tumor suppressor genes and similar drugs are now in development (Braiteh et al., 2008 ; Phillips, 2008 ).

As explained, every cell in the organism carries an identical genome, however, despite the stability of these instructions, the terminal phenotype within an organism is not fixed and deviation is caused by gene expression changes in response to environmental cues. DNA methylation, histone modification and RNA-associated silencing are the major ways these changes are controlled, which are described in more detail below. The methylome is the genomic distribution of methylated DNA sequence present in a cell and is capable of undergoing modification with respect to the environment or the developmental stage. DNA methylation involves the covalent addition of a methyl group at position 5 of the pyrimidine ring of cytosine that is represented as 5-methyl C or C Me . Transcription of most protein coding genes in mammals is initiated at promoters rich in CG sequences, where cytosine is positioned next to a guanine nucleotide linked by a phosphate called a CpG site. Such short stretches of CpG-dense DNA are known as CpG islands. In the human genome 60–80% of 28 million CpG dinucleotides are methylated (Lister et al., 2009 ; Ziller et al., 2013 ). Chromatin structure adjacent to CpG island promoters facilitates transcription, while methylated CpG islands impart a tight compaction to chromatin that prevents onset of transcription and therefore, gene expression. In CpG islands active C's are normally unmethylated and when an unmethylated cytosine spontaneously deaminates to uridine, it is converted back to cytosine by DNA repair mechanisms, thus preserving CpG sequences through evolution. The presence of 5-methyl C in a CpG island denotes an inactive promoter owing to the condensation of chromatin triggered by DNA methylation. CpG sites are methylated by one of three enzymes called DNA methyltransferases (DNMTs). A variety of DNMTs are responsible for DNA methylation patterns established during embryogenesis. One type of DNA methyltransferase, DNMT1, is responsible for maintaining normal methylation patterns by copying them exactly between cell generations during replication. DNMT2 is associated with embryonic stem cells and potential RNA methylation. DNMT3a and DNMT3b are involved in de novo DNA methylation at CpG sites (Clouaire and Stancheva, 2008 ; Singh and Li, 2012 ). Histones are the core protein components of chromatin complexes, and they provide the structural backbone around which DNA wraps at regular intervals generating chromatin. The nucleosome represents the first level of chromatin organization and is composed of two of each of histones H2A, H2B, H3, and H4, assembled in an octameric core with DNA tightly wrapped around the octamer (Luger et al., 1997 ). Histones regulate DNA packaging with immense influence on the degree of chromatin compaction, influencing transcriptional activity as well as transcriptional silencing. Histone modifications are post-translational changes on the histone tails, that are flexible stretches of N or C terminal residues extending from the globular histone octamer. Modifications of histones include acetylation of lysine residues, methylation of lysine and arginine residues, phosphorylation of serine and threonine residues, and ubiquitination of lysine residues present on histone tails, as well as sumoylation and ADP ribosylation. All of these changes influence DNA transcription. Addition or removal of methyl groups on DNA (see above) and histones and acetyl groups on histones are the prime mechanisms of changing the epigenetic landscape (Cedar and Bergman, 2009 ). Histone acetylation is carried out by enzymes called histone acetyltransferases (HATs), that are responsible for adding acetyl groups to lysine residues on histone tails while histone deacetylases (HDACs) are those that remove acetyl groups from acetylated lysines. Generally, presence of acetylated lysine on histone tails leads to a relaxed chromatin state that promotes transcriptional activation of selected genes; in contrast, deacetylation of lysine residues leads to chromatin compaction and transcriptional inactivation. RNA-associated silencing is a type of post-transcriptional gene modification during which the expression of one or more genes is downregulated or suppressed by small non-coding stretches of RNA, sometimes called microRNAs (miRNA) and small interfering RNAs (siRNA). Although microRNAs only represent 1% of the genome they have been estimated to target 30% of genes (Lewis et al., 2005 ). These RNAs can act as switches and modulators, exerting extensive influence within the cell and beyond. These RNAs fine-tune the gene expression as they act as specific modulators based on cell-type specificity of the organism during development as well as pathological conditions (Giraldez et al., 2005 ; Girardot et al., 2012 ; Baer et al., 2013 ). Also, miRNAs have been known to play a role in tumor suppression, apoptosis, cellular proliferation and cell movement which suggests that they can be manipulated in treating epigenetic diseases like cancer (Kala et al., 2013 ). Putative mechanisms of RNA silencing include the ability of non-coding RNA to negatively regulate expression of target genes at the posttranscriptional level by binding to 3′-untranslated regions of target mRNAs resulting in their degradation (Singh et al., 2008 ). All genes in every cell type are activated or silenced by an underlying interplay between these described epigenetic mechanisms. And as explained in the Introduction, exogenous epigenetic forces modify the endogenous inherited epigenetic pattern. In order to illustrate the endogenous epigenetic regulation of a gene, we will use the example of OCT4. OCT4 is the master pluripotency gene, which is regulated through different stages of human development, and its activation is necessary for maintaining pluripotency, whereas it must be silenced in order for a cell to differentiate (Kellner and Kikyo, 2010 ) (Figure 2 ). OCT4 is thus active in embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) as well as in cancer cells, but is silenced in differentiated cell types. The three types of epigenetic modifications explained above i.e., DNA methylation, histone modification and RNA silencing are responsible for such regulation of OCT4 gene expression. This has been illustrated in detail along with the various epigenetic tags involved in its regulation in Figure 2 . Epigenetic regulation of OCT4 in stem cells, cancer cells and somatic cells . The figure represents the various epigenetic mechanisms involved in regulating the gene expression of OCT4. (A) This section represents the structure of the OCT4 gene. The green bar represents the coding region. The beige bar represents the upstream region containing regulatory sequences. The four pink bars represent conserved regions; CR1 (−129 to −1), CR2 (−1510 to −1315), CR3 (−1956 to −1852), CR4 (−2557 to −2425) (data for human OCT4 gene). The green triangles represent the sites for binding of activators and the red squares represent the sites for binding of the repressors and these sites lie within the enhancers and promoter. +1 denotes transcription start site (TSS). (DE, Distal Enhancer −2057 to −1955; PE, Proximal Enhancer −1152 to −901; PP, Proximal Promoter −240 to +1) (This data is for the OCT4 gene from mouse ESCs since information for human OCT4 was insufficient). (B) This section represents the regulation of OCT4 in ESCs and iPSCs. OCT4 is highly expressed in these cells. Binding of transcriptional machinery induces OCT4 expression. This can be attributed to the hypomethylated promoter, enhancer region, which promotes binding of transcriptional activators and co-activators like Pcaf, LRH−1, SF−1, and Brg1 sub-unit of the SWI-SNF nucleosome-remodeling complex, which in turn facilitates the binding of RNA polymerase II. Activating histone marks like H3K4me and H3K9Ac are found on the histones surrounding the regulatory regions of the gene and they enhance the recruitment and binding of transcription factors thus inducing gene expression. (C) This section represents the regulation of the OCT4 gene in cancer cells, where similar to embryonic-like cells, it is highly expressed. In the case of hepatocellular carcinoma, an additional layer of epigenetic regulation is seen with the activity of the OCT4-pseudogene (pg)4, a non-coding RNA that protects the OCT4 transcript from inhibition by miRNA-145. Thus, OCT4-pg4 indirectly enhances the expression of OCT4 in cancer cells by acting as a protective shell for nascent OCT4 transcripts. The activity of the Brg1 sub-unit of the SWI-SNF complex is not necessary for OCT4 expression in cancer cells. (D) This section represents the regulation of OCT4 in somatic cells, which are differentiated and have a specialized function. Here OCT4 expression is repressed because of the hypermethylated promoter region and the repressive H3K27me and H3K9me marks. This results in compaction of the regulatory regions and facilitates the recruitment of other transcriptional repressors like RAR, GCNF, COUP-TFs, further compacting the regulatory regions, and making it inaccessible to the transcriptional machinery. SNF5, a core sub-unit of the BAF complex (SWI-SNF) acts as a switch between pluripotency and differentiation and promotes differentiation by binding to regulatory regions of OCT4. In addition, the sumyolation of orphan nuclear receptor Tr2 at Lys 238 results in its release from promyelocytic (PML) nuclear bodies. (In ESCs and iPSCs Tr2 is bound to PML nuclear bodies and acts as an activator). This in turn results in an exchange of co-repressor Rip-140 for co-activator Pcaf, making Tr2 a repressor. Also, miR-290 through miR-295 enhance methylation as they inhibit Rb12, which would otherwise inhibit the activity of de novo methyl transferase Dnmt 3a/3b. In a similar way, let us consider the effect of exogenous epigenetic forces on the expression of OCT4. Vitrification, which is a commonly used method for cryopreservation, has been documented to alter the methylation patterns of the OCT4 gene. In two such cases, vitrification resulted in decreased methylation of the OCT4 promoter causing reduced gene expression in mouse blastocysts and the same was observed for mouse oocytes that underwent vitrfication followed by in vitro maturation (Milroy et al., 2011 ; Zhao et al., 2012 ). This explains how the external environment, in this case temperature, can lead to alteration of the epigenetic profile of one or many genes, ultimately causing differential gene expression. The effects of an epigenetic factor can be manifested as a global change in DNA methylation affecting multiple genes, or modified expression of very specific genes. The mechanisms and cellular pathways that are involved in the creation of these global or specific epigenetic changes are currently obscure. Below we describe a working hypothesis on how these changes might occur. We propose that an epigenetic factor can act through either a direct or an indirect mechanism (Figure 3 ). A direct effect could happen in two ways; which we term Type 1 and Type 2. Type 1 direct effect occurs when the epigenetic factor directly alters the state of epigenetic enzymes—either by binding to them and preventing them from carrying out their normal function, damaging them in some other way, or upregulating them. The altered bioavailability of epigenetic enzymes then results in aberrant recruitment of epigenetic tags to promoters and enhancers on a genome-wide scale. Such a direct effect would be effective across the entire genome, not affecting any specific gene but resulting in a randomly altered epigenome. An example of a directly acting epigenetic factor is the antihypertensive hydralazine, which inhibits DNA methylation. The direct and indirect epigenetic pathway . The figure represents two different routes through which an epigenetic factor can modify the epigenome leading to altered gene expression. Epigenetic effects exerted by an external factor or intrinsic environment can lead to direct and indirect effects on the epigenome. Green represents direct effects of an epigenetic factor and red represents indirect effects of an epigenetic factor. The direct pathway can operate in two different ways; namely Type1 and Type 2. In the Type 1 direct pathway, the epigenetic factor directly exerts an effect on the epigenetic enzymes such as DNMTs, HDACs, HATs, HMTs, HDMs, etc. such that there is an altered bioavailability of these enzymes in the cell. A Type 2 direct effect is when an epigenetic factor interferes with a biochemical pathway such that there is altered availability of a metabolite required for constituting an epigenetic tag. Both cases can result in aberrant or inadequate recruitment of epigenetic tags in a random fashion to non-specific promoters, ultimately establishing an altered epigenetic profile. In the indirect pathway, the epigenetic factor indirectly exerts an effect on the epigenome by first interfering with any signaling pathways of the cell. An acute exposure to the epigenetic factor can cause altered expression of growth factors, receptors, ion channels and so on resulting in non-homeostatic cellular processes. This in turn might lead to an altered status of transcriptional machinery (bound or unbound to the promoter/enhancer) and its bioavailability in a cell. A chronic exposure to the epigenetic factor might lead to retention of such state of transcriptional machinery (bound or unbound to the promoter/enhancer) causing altered gene expression as well as aberrant recruitment of epigenetic enzymes, leading to permanent addition or removal of epigenetic tags to specific promoter/enhancers. This consequently establishes an altered epigenetic profile. Type 2 direct effects occur when an epigenetic factor causes a change in a biochemical process that results in an altered availability of a substrate, intermediate, by-product or any other metabolite participating in the biochemical pathway, that is used to make up epigenetic tags (for example acetate). This in turn leads to altered availability of epigenetic tags, in this case acetyl groups on histones, which leads non-specific modification of the epigenome (Figure 3 ). The second major way that factors can cause epigenetic changes is by what we term indirect mechanisms (Figures 3 , 4 ). A biphasic mechanism is postulated for indirect effects in which acute exposure to a factor influences cellular signaling pathways that leads to altered expression of growth factors, receptors and ion channels, which in turn alter transcription factor activity at gene promoters. With more chronic exposure, the transcription factors and other gene regulatory proteins, in addition to altering gene expression activity, actually recruit or repel epigenetic enzymes to/from the associated chromatin, resulting in the addition or removal of epigenetic tags (Figure 4 ). In this way cells adapt to the persistent gene expression changes by causing permanent modifications to DNA methylation and chromatin structure, leading to enduring alteration of the affected epigenetic network (Figures 3 , 4 ). An example of an indirectly acting factor is the drug isotretinoin, which has transcription factor activity. The indirect epigenetic pathway . An epigenetic factor operating through an indirect pathway interferes with transcriptional machinery. Chronic exposure to an epigenetic factor can lead to the retention of an already altered state of transcriptional machinery. The transcriptional machinery (bound or unbound to the gene regulatory regions i.e., promoters/enhancers) includes a number of proteins like transcription factors, activators and co-activators, repressors and co-repressors and nucleosome or chromatin remodeling complexes. For simplicity, these proteins are Fectively termed as “Gene regulatory protein” for this figure. (A) A gene regulatory protein might affect the status of RNA Polymerase (1) By inhibiting it from binding to a transcriptional apparatus or forming one or (2) by facilitating the binding of RNA Polymerase as well as formation of a transcriptional apparatus essential for the initiation of transcription. (B) A gene regulatory protein might also affect the status of epigenetic enzymes like DNMTs, HDACs, HATs, HMTs, HDMs, etc., which are responsible for the addition or removal of epigenetic tags (methyl group on DNA or histone, acetyl group on histones) on gene regulatory regions. This can be (1) By inhibiting epigenetic enzymes from binding to the gene regulatory regions and hence prohibiting the addition or removal of epigenetic tags (2) By facilitating the binding of epigenetic enzymes to gene regulatory regions and hence allowing the addition or removal of epigenetic tags. Such retention of a gene regulatory protein due to chronic exposure to an epigenetic factor might result in a permanent change in the epigenetic profile and/or gene expression of a specific gene affected by that epigenetic factor through an indirect pathway. Epigenetic factors known to cause such direct and indirect effects are well-documented but their exact mechanism has not been accurately elucidated. For example, nutritional interventions in adulthood like caloric restriction can induce epigenetic changes that have the potential to alleviate age-related diseases (Bacalini et al., 2014 ). In caloric restriction food intake is intentionally reduced by 30–50% (Zakhari, 2013 ) and has been shown to delay the aging process in mice by decreasing the levels of histone deacetylase 2 (HDAC2) which otherwise increases during the normal aging process (Chouliaras et al., 2013 ). Thus, this is an example of direct effect by an epigenetic influence (caloric restriction). Another example is curcumin, a polyphenol found in turmeric, which can be regarded as a dietary epigenetic factor. It is an inhibitor of the Histone acetlytransferase p300/CBP (co-activator) and GATA4 (a zinc finger transcription factor), which leads to decrease in nuclear acetylation induced during myocardial cell hypertrophy (Morimoto et al., 2008 ). The possible mechanisms through which curcumin exerts such an effect might be through allosteric regulation of p300 or through interfering with nuclear signaling pathways like transcriptional activation by NF-κB (Morimoto et al., 2008 ). Hence the epigenetic effect of curcumin is an example of a combined direct and indirect effect.

We have presented a comprehensive narrative of the role of both endogenous and exogenous epigenetic influences on the human lifespan. The future of epigenetics holds tremendous promise for understanding the complexities involved in genetic regulation, cellular differentiation, aging and disease; and a more complete and comprehensive understanding of the mechanisms that underlie the formation and erasure of epigenetic marks could allow us to commandeer the process and possibly fine tune the human epigenome. Ultimately, continued efforts to determine how and when epigenetic switches regulate gene function will elucidate the interplay between the genome, the epigenome, and the environment and facilitate the development and optimization of novel therapeutic tools. In terms of future application, full understanding of these mechanisms will ultimately revolutionize personalized medicine. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

For the past several decades genetics has been at the forefront in terms of understanding human disease. A recent addition to genetics has been epigenetics, which includes the role of the environment, both social and natural, including day-to-day habits, lifestyle and personal experiences on human health. Epigenetics establishes a scientific basis for how external factors and the environment can shape an individual both physically and mentally. The knowledge that environment and lifestyle can alter health brings with it awareness that habits, social environment, diet and other factors shape health beyond our acquired genetic traits. Moreover, despite the risk presented by inherited genes and mutations, epigenetic factors play a decisive role in the actual development of disease. Research into epigenetics could lead to insights into how factors like diet and exercise can be customized to an individual in concordance with their naturally inherited genome in order to minimize the risk of developing a disease to which he/she is naturally predisposed. Advances in epigenetic profiling technology such as genome-scale DNA methylation analysis points to the future possibilities of how epigenetic profiling can help in determining the risk of an individual with a particular type of genetic makeup developing a specific disease. Also the same epigenetic profile, along with knowledge of the genomic sequence, can help to determine which medications or alternative medicine approaches would be effective in preventing or curing a particular disease. Such approaches toward improving health and lifestyle and reducing the risk of developing an otherwise inevitable disease might be possible in the near future. It will require extensive knowledge of the biochemical and physiological mechanisms of epigenetics, and we are still on this challenging path, but we have good reasons to be optimistic.

The literal meaning of the term epigenetic is “on top of or in addition to genetics.” The series of chemical tags that modify DNA and its associated structures constitute the epigenome, and include any genetic expression modifier independent of the DNA sequence of a gene. The genome defines the complete set of genetic information contained in the DNA, residing within the cells of each organism. The epigenome, on the other hand, comprises the complex modifications associated with genomic DNA, imparting a unique cellular and developmental identity. The epigenome integrates the information encoded in the genome with all the molecular and chemical cues of cellular, extracellular, and environmental origin. Along with the genome, the epigenome instructs the unique gene expression program of each cell type to define its functional identity during development or disease (Rivera and Ren, 2013 ). The epigenome also, in some sense, represents the ability of an organism to adapt and evolve through expression of a set of characteristics or phenotypes developed in response to environmental stimuli. Thus, in contrast to the consistency of the genome, the epigenome is characterized by a dynamic and flexible response to intra- and extra-cellular stimuli, through cell-cell contact, by neighboring cells, by physiology, or entirely by the environment that the organism is exposed to Figure 1 . Cytokines, growth factors, alterations in hormonal levels as well as release of stress-response and neurotropic factors are some examples of molecules that are modulated by the environment and which come under the category of epigenome modifiers. Ultimately, the environment presents these various factors to the individual that influence the epigenome, and the unique epigenetic and genetic profile of each individual also modulates the specific response to these factors (Figure 1 ). A compilation of epigenetic influences on humans . The figure represents a compilation of the various epigenetic influences on humans by different sources present in the environment. While some of these might be beneficial for health and behavior, others might be harmful and interfere with the body and mind creating an imbalance, which might manifest as a disease or psychological disorder. Some of the beneficial influences listed are exercise, microbiome (beneficial intestinal bacteria), and alternative medicine whereas harmful influences include exposure to toxic chemicals and drugs of abuse. Factors such as diet, seasonal changes, financial status, psychological state, social interactions, therapeutic drugs, and disease exposure might have beneficial or harmful effects depending on the specific nature of the influence. The environment thus complements and shapes human health. With the help of extended research in the field, we might be able to steer these influences in a positive way. Enzymatic activity in response to the environment promotes addition or removal of epigenetic tags on DNA and/or chromatin, sparking a cavalcade of changes that affect cellular memory transiently, permanently or with a heritable alteration. Some of the molecular mechanisms involved in this process are explained in more detail below.

Many transgenerational phenotypic inheritance profiles cannot be explained by the normal human mutation rate of 2.3 × 10 −8 per nucleotide per generation (Arnheim and Calabrese, 2009 ). The reason for this discrepancy is that epigenetic changes most likely contribute to the majority of these transgenerational effects. Transgenerational epigenetic inheritance was first observed in plants (Manning et al., 2006 ), however, it has also been reported in rodents and humans (Carone et al., 2010 ). Heritability of epigenetic expression is demonstrable where multiple generations are simultaneously exposed to the same environmental conditions that include diet, toxins, hormones, etc. (Curley et al., 2011 ; Vassoler et al., 2013 ). In such a model, the mother = first generation, the fetus = 2nd generation, the reproductive cells of fetus = 3rd generation, and the future offspring of fetus = 4th generation. In order to provide a convincing case for trans-generational stability, an epigenetic change must be observed in the 4th generation (Hughes, 2014 ). Recent studies have shown that maternal methyl-donor supplementation affects not only the mother, but is also inherited in the F2 generation through germline epigenetic modifications (Duhl et al., 1994 ; Wolff et al., 1998 ; Morgan et al., 1999 ; Cropley et al., 2006 ). Transgenerational epigenetic influence of longevity has also been shown in C. elegans (Greer et al., 2011 ).