Cardiovascular diseases (CVDs), diabetes, obesity and cancer are polygenic Singh RB, Niaz MA: Genetic variation and nutrition in relation to. Manhattan plot showing association between methylation at individual CpG sites DNA methylation, ↑ histone acetylation and ↓ histone methylation. Obesity. Recent advances of whole-genome association studies have led to the identification of common DNA sequence variants associated with obesity and Type 2.
Various modifications to the amino terminal tails of the histone proteins that package DNA in the nucleus of each cell are known to be highly correlated with transcriptional activity and chromatin structure and therefore clearly play a role in regulating gene expression potential.
However, as pointed out by Henikoff and Shilatifard and others, it remains unclear whether histone modifications have the definitive epigenetic characteristics of mitotic heritability, that is, whether specific established histone modifications can convey information over mitosis.
On the other hand, autoregulatory transcription factors have been recognized for decades as being able to function epigenetically Riggs and Porter,yet they receive very little attention these days, Waterland observed.
For example, the MyoD transcription factor, which plays an important role in muscle development in mammals, binds to and regulates its own transcription. During cell division, once MyoD is turned on, the MyoD protein, which is in the nucleus, is partitioned to both daughter nuclei, perpetuating its feed-forward auto-regulation.
Many other transcription factors work in the same fashion. Finally, noncoding RNA, another epigenetic mechanism, works in a similar way in terms of being partitioned in the nuclei during mitosis and being delivered to both daughter cells.
Waterland emphasized that all of these mechanisms and potentially others as well work in a synergistic fashion to maintain different regions of the chromatin in either a more transcriptionally silent or more transcriptionally active state.
Of all the various potential epigenetic mechanisms, Waterland observed that most of the presentations at the workshop would focus on DNA methylation. First, DNA methylation is the most stable epigenetic mark, making it a very good candidate for conveying the type of long-term memory effects of relevance within the context of the developmental origins paradigm. Additionally, researchers understand its mechanism of mitotic heritability, knowledge of which makes it a bona fide epigenetic mark, in Waterland's opinion.
Moreover, it can be measured in a molecule-specific fashion, allowing for precise quantitation of the genetic influences on epigenetic outcomes. To provide some background on DNA methylation, Waterland explained that, first, most cytosines within CpG dinucleotides are methylated at the number 5 position, converting cytosine to methyl-cytosine, a covalent modification that affects gene expression by regulating the affinity of methylation-sensitive DNA-binding proteins.
Another feature of DNA methylation to keep in mind is that tissue-specific patterns of CpG methylation are established during development.
Shortly after fertilization, the vast majority of methylation in both the sperm and egg genome is erased. Then, at about the time of the early embryo's implantation, methylation patterns are reestablished in a lineage-specific manner as part of the differentiation process.
The reestablishment process proceeds during fetal development and even during postnatal life. Yet another feature of DNA methylation is that it requires dietary methyl donors and cofactors. And finally, and very importantly in Waterland's opinion, DNA methylation is mitotically heritable and researchers understand the mechanism underlying its mitotic heritability.
He explained that a CG sequence on one strand is also a CG sequence in the opposite direction on the other strand, allowing for semiconservative replication of established DNA methylation patterns during mitosis. Waterland discussed evidence—mostly from animal models but also from humans—demonstrating how epigenetic mechanisms can affect obesity.
For example, when mice and other mammals are cloned, they often are born with a slightly elevated weight and develop adult-onset obesity. Waterland showed an image from Tamashiro et al. In humans, the neurodevelopmental syndrome known as Prader—Willi syndrome is a good example, in Waterland's opinion, of an epigenetic dysregulation that can cause obesity. Although the syndrome is most commonly caused by a genomic deletion of a large portion of chromosome 15, a subset of sporadic cases are caused by epigenetic silencing of the same genomic region.
Agouti mice are a third example of epigenetic dysregulation known to cause obesity. Again, Waterland showed an image of two genetically identical mice, this time two newborns who were indistinguishable at birth but who, because of an epigenetic difference at the agouti viable yellow Avy locus, grew up into very different phenotypes.
One grew up to be yellow and obese, the other brown and lean see Figurewith the obese mouse having a very low level of DNA methylation at the Avy locus and her lean sister being very highly methylated at the same locus. Alleles that behave like the Avy, that is, with dramatic inter-individual variation in DNA methylation even among genetically identical individuals, are called metastable epialleles. Waterland and others have shown that nutrition and other environmental stimuli, both before and during pregnancy, can affect the establishment of DNA methylation at metastable epialleles with persistent and permanent phenotypic consequences.
A fascinating feature of metastable epialleles, in Waterland's opinion, is the systemic nature of the inter-individual variation, with essentially the same level of methylation present in all of the different cells of the body. Consequently, one could take a drop of blood from an agouti mouse, measure the methylation at Avy, and predict with absolute certainty whether the mouse would become obese in adulthood. Obstacles to Understanding the Epigenetic Contribution to Human Obesity While many clinicians and epidemiologists would like to have an epigenetic biomarker in humans like the differentially methylated Avy locus in agouti mice that could be used to predict who will become obese, Waterland cautioned that finding such a marker will not be a simple task.
He identified several obstacles to understanding how epigenetic dysregulation contributes to human obesity, not the least of which is that genetic variation is an important determinant of epigenetic variation. If one was to conduct a case control study of obese versus lean individuals, one could certainly find epigenetic differences between the two groups, he said. However, it would be difficult to rule out that the observed differences in epigenetic regulation and obesity were caused by genetic differences between the two groups.
Another obstacle to understanding the epigenetic contribution to human obesity is the largely cell type—specific nature of epigenetic regulation. Although clinicians and epidemiologists would like to be able to study DNA from easily obtainable samples e. Yet another obstacle is poor characterization of epigenetic regulatory regions, though the situation is improving, Waterland observed.
One of the biggest insights provided by those data, in Waterland's opinion, is the importance of epigenetic regulation in enhancer regions.
Most epigenetics researchers have been focused over the past couple of decades on promoter regions, that is, regions at the beginnings of genes. Enhancers are regulatory regions often located hundreds of thousands of base pairs away from genes.
It appears now that epigenetic regulation at enhancers plays a critical role in tissue-specific and cell type—specific gene expression. In Waterland's opinion, inferring tissue-specific epigenetic dysregulation is going to be very difficult in human studies. Also with respect to the poor characterization of epigenetic regulatory regions, while the general rule is that DNA methylation is a silencing mechanism, Yu et al.
The best example, in Waterland's opinion, is in cancer epigenetics.
Epigenetics and obesity
It has been known for decades that tumors are characterized by dramatic epigenetic dysregulation. However, it was unknown until recently whether epigenetic dysregulation actually caused the cancer. With respect to obesity, when epigenetic changes are observed in lean versus obese individuals, the direction of causality is still unclear.
Imprinting disorders associated with obesity: Individuals affected by PWS have cognitive impairments and struggle with a voracious and uncontrollable appetite, which is often associated with the development of severe obesity within the first 6 years of life. The strong desire for food appears to result from a satiety dysfunction in the CNS [ 36 ].Rhonda Patrick: Nutrigenomics, Epigenetics, and Stress Tolerance
This neurogenetic disorder arises from an imbalanced expression of gene products and transcripts mapping to chromosome 15qq The genomic region carries parental-specific methylation imprints and in most cases the epigenetic program imprinted on the maternally inherited chromosome cannot compensate for paternal 15qq13 deletions, which are the most frequent cause of PWS [ 37 - 39 ].
The GNAS locus — both in mouse and human — provides intriguing support for the kinship theory of genomic imprinting. The elevated metabolic rate of these adult mouse mutants is thought to result from a deregulation in energy balance and sympathetic nerve activity [ 4142 ]. Tissue-specific expression correlates with allele-specific differences in histone methylation [ 47 ].
This metabolic phenotype can be rescued by deletion of a differentially-methylated imprinting control region on the paternal allele. Genetic as well as epigenetic abnormalities of the human GNAS locus are also associated with metabolic disorders such as pseudohypopara thyroidism and Albright's hereditary osteodystrophy AHO [ 46 - 51 ]. The abnormalities do not entirely parallel the mouse mutant phenotypes, but do have some common features.
AHO individuals generally have a short, obese body stature [ 52 ]. The above examples illustrate the potential of disregulated genomic imprints to promote functionally opposing effects in energy homeostasis: But the question remains: Subtle imprinting effects in mice influencing body weight Results from a recent genome-wide mapping approach suggest that genomic imprinting can influence variation in body composition of adult mice [ 53 ]. In their study, Cheverud and colleagues identified imprinted quantitative trait loci iQTL in regions of the mouse genome that previously were not known to be imprinted [ 53 ].
Morison and colleagues suggested that numerous imprinted genes with subtle effects remain to be discovered, and that these genes will not map to major, genomic imprinting clusters identified so far in mice and humans [ 54 ]. Indeed, estimates of the number of imprinted genes and genomic loci vary greatly [ 2954 - 57 ]. Although parental imprinting occurs in all therian mammals and the molecular mechanism is conserved for many genes, including the IGF2-H19 locus [ 58 ], there is discordance among species in the number of imprinted genes [ 54 ].
Disparity in litter size between mouse and human is one factor that possibly contributes to the discordance of imprinted genes [ 59 ].
- The Role of Epigenetics in the Etiology of Obesity: A Review
Although the mouse is an excellent and tractable model organism in which to study epigenetic deregulation of imprinted genes per se, the discordance between mouse and human in both the number and identities of imprinted genes [ 535759 ] limits the utility of mouse for studying the role that deregulated genomic imprinting could play in human obesity. Based on computer-learning algorithms that recognize certain DNA sequence characteristics such as concentration of repeated elements and recombination hotspots, Luedi and colleagues recently predicted parental imprinting of approximately humans genes [ 5657 ].
For the vast majority of these potentially imprinted genes, differential epigenetic marks have not yet been identified and expression patterns reflecting parent-of-origin specificity await demonstration. Nevertheless, these early findings hint that subtle imprinting effects may also contribute to variation in body mass in humans. Below, that possibility is explored. Undiscovered parental imprints in humans?
Genetic and epigenetic abnormalities in regions of the human genome, known to undergo parental imprinting are predominantly associated with distinct developmental and pathological phenotypes [ 3760 - 62 ]. These phenotypes and their unusual inheritance patterns are often the only evidence of a parental imprint and have, in this way, guided the mapping and identification efforts for many of the currently known imprinted loci in humans.
Therefore, it is therefore plausible that other, as yet unidentified imprinted genes, could contribute to subclinical variations in phenotype, including body weight. A number of genome-wide linkage analyses have been carried out, with the goal of identifying new genomic loci that harbor parent-of-origin effects that influence body weight. Lindsay and colleagues detected regions on maternally-derived chromosomes 5 and 6, and paternally-derived chromosome 10 with tentative evidence of imprinted genes that might influence the risk of Type 2 diabetes or obesity in Pima Indians [ 63 ].
In a follow-up study, it was reported that the birth weight in the Pima population appears to be influenced by loci on the paternally-inherited chromosome 11 [ 64 ]. Screening DNA samples from African—American, European—American and German individuals, Price and colleagues found evidence for at least three different obesity-related genetic loci with parental effects [ 65 ]. In their genome-wide linkage analysis a paternal effect for BMI was detected for region 13q32, and locations on chromosomes 10p12 and 12q24 suggest a maternal effect on BMI.
None of these three loci had been known previously to harbor genomic imprints [ 65 ]. The results of two similar genome-wide scans have also provided evidence for the existence of potentially imprinted loci influencing body weight [ 6667 ].
Common to all of these studies is the feature that many of the newly mapped loci have not previously been reported as imprinted, and were not detected in the screens performed by other laboratories.
With the provision that a parent-of-origin effect does not necessarily provide direct evidence of imprinting [ 68 ], these genome-wide studies suggest the existence of many more genomic loci affecting body weight that are perhaps controlled by epigenetic mechanisms. The young patients normally require insulin therapy during the first 3 months of life after which remission occurs. Umbilical hernia, macroglossia and learning difficulties are variable but distinct nondiabetic manifestations of the 6q24 disorder.
Mosaic hypomethylation at multiple imprinted loci HIL was found to be a recurrent, genomic feature in a cohort of individuals that experienced TND and these epigenetic lesions were more prevalent in nonleukocyte cells, such as buccal cells and fibroblasts [ 69 ]. Mutations in ZNF57, a gene encoding the zinc finger binding protein 57, have recently been associated with this autosomal, recessive imprinting disorder [ 70 ], and the basis for aberrant methylation-mosaicism might be established during early embryogenesis, a developmental stage when ZNF57 is normally expressed [ 70 ].
Epigenetic mosaicism among tissues and cells is a phenomenon observed in many species, including humans [ 71 - 75 ]. For instance, epigenetic defects such as loss of imprinting LOI of the IGF2 gene is a common event in Wilm's tumor and lung, breast and ovarian cancers and gliomas where the normally silent, maternal allele of this growth-promoting gene is aberrantly activated [ 7677 ].
Our ability to investigate this possible connection, however, is only as good as our ability to detect epigenetic abnormalities through screening methods typically applied to the general population.
It is possible that subtle imprinting abnormalities — specifically, those that result from epigenetic mosaicism among cells and tissues — have remained undetected in the general population because epigenetic lesions were limited to tissues other than those analyzed. For example, DNA methylation patterns could indicate normal parental imprints during a screen of peripheral blood leukocytes, a common DNA source, while epigenetic defects in white adipose tissue would stay unnoticed.
In addition, methods for the detection of DNA methylation, such as methyl-sensitive PCR, may not be adequate for obesity research. Although some of these methods are very sensitive and enable the detection of 0. For instance, the density of DNA methylation at the human leptin promoter is highly variable among alleles and cells from an individual [ 80 ]. While the effect of this mosaicism on gene expression awaits demonstration, it is likely that such methylation differences would go unnoticed by many of the current assays employed to assess epigenetic variations.
Thus, tissues to be sampled and techniques to be applied are important factors to be considered for obesity research. With these high-throughput methods it will be possible to detect subtle irregularities in DNA methylation patterns among individual DNA molecules, cells and individuals. Similarly, next-generation sequencing technology, in combination with chromatin immunoprecipitation ChIP-Seq [ 8384 ], will also provide a detailed picture of the histone modifications in genomic regions that are associated with deregulated energy metabolism.
Although this sequencing technology has not yet advanced to the level where an individual's entire genome can be routinely scanned for subtle epigenetic differences, the data produced with these new techniques will soon advance our currently limited understanding of the epigenetic underpinnings of obesity. What could be the cause of these imprinting differences among individuals?
Environmental stimuli and stresses can alter epigenetic modifications and gene expression [ 7887 - 89 ]. Indeed, abnormal epigenetic patterns at imprinted loci were one of the first indications that external environmental stimuli can influence an individual's epigenome. Manipulation of embryos and embryonic stem cells, routinely employed in assisted reproductive technologies in humans, as well as mammalian cloning and gene-targeting procedures have been found to affect the epigenetic status of imprinted loci [ 878890 ].
Environmental changes are inevitable during such procedures, insofar as cells and embryos are physically moved and become exposed to unnatural growth conditions. These environmental stresses — occurring during a limited period of time at the earliest stages of development — frequently influence the resulting adult phenotype [ 91 - 94 ].
It has been suggested that an elevated risk of Beckwith—Wiedemann syndrome, a fetal overgrowth and imprinting disorder, results from manipulations that occur during in vitro fertilization [ 95 - 98 ], although donor oocyte quality has not been ruled out as an independent risk factor.
Abnormal birth weights, both low and high, are frequently observed in animals and humans that have experienced early-embryonic interventions [ 87 ]. These phenotypic variations are often associated with altered gene expression and changes in DNA methylation patterns at imprinted loci [ 99 - ].
Nutrition is an external, environmental signal directly relevant to obesity, and it can affect gene expression at imprinted loci. Similarly, a methyl-deficient diet significantly increases the expression of the imprinted, paternally expressed gene encoding the insulin-like growth factor 2 Igf2 in the prostate of mice and decreases the repressive dimethyl-H3K9 histone modification at this imprinted locus [ ].
The Igf2 locus appears particularly susceptible to external, nutritional signals, as Waterland and colleagues reported that subtle dietary changes during the post-weaning phase of mouse development induces permanent changes in DNA methylation and altered expression at the Igf2 locus [ ]. The notion that nutritional interventions can induce DNA methylation changes has garnered considerable interest, both within the research community and with the public [ ]. However, considering that much effort has been applied in finding such methylation changes — at imprinted loci in particular — the results to date are rather modest and more results are still anticipated that would demonstrate how nutritionally induced epigenetic alterations affect the expression of specific genes that are directly involved with resource allocation of an organism.
This locus is different from those described above, insofar as it does not carry a parental-specific imprint. The biology that underlies this association is slowly being resolved. One relevant factor, which modulates this epigenetic profile, is the environmental influence on the epigenetic marks that can lead to obesity remain rather rudimentary.
For example, the FTO gene codes for an enzyme that is capable of removing methyl groups from DNA [ 33 ] and a long-term exposure to the high-fat diet may decrease methylation of the melanocortin-4 receptor gene MC4R [ 40 ]. Obesity induced by a high-fat diet can modify the methylation patterns of leptin Milagro et al. In one study it was observed that methylation of the regulatory DNA of the essential fatty acid binding protein in lipid metabolism was also associated with traces of the metabolic syndrome in individuals in more than 40 families [ 41 ].
In a study carried out by Lima et al.
Epigenetics and obesity
Results of this research may be used in the future in the prevention and management of complications of obesity, since the ADRB3 gene was related to obesity. Several other genes involved in adiposity have promoters that appear to be epigenetic targets for obesity epi-obesogenic genes.
One of the first genome-wide methylation studies revealed increased methylation levels at one CpG site UBASH3A gene and reduced methylation levels at one CpG site TRIM3 gene in obese individuals compared to controls, providing evidence that obesity is associated with epigenetic changes [ 44 ].
Although collectively, such studies could indicate that epigenetic changes are associated with obesity, it is not really clear whether they predict or precede obesity [ 45 ]. Since obesity arises from combined effects between genes, environment and behavior, the study of epigenetics comes to identify genes that can determine the susceptibility of individuals to obesity by providing pathophysiological mechanisms for weight regulation, food intake control and fat distribution.
And thus, improve public policy actions and guidelines to better guide strategies for prevention and treatment of obesity.
Acknowledgements We thank all the authors and collaborators for contributing with this publication. All authors read and approved the final manuscript. Competing Interests The authors declare that they have no competing interests. A Mendelian Randomization Approach. Fact sheet N Neurosci Biobehav Rev Dev Period Med Trends Pharmacol Sci J Diabetes Res Prog Mol Biol Transl Sci A review of molecular mechanisms and the evidence for folate's role. Prog Lipid Res Proc Nutr Soc Brief Funct Genomics Horm Metab Res Indian J Med Res Nat Rev Dis Primers 3: Current Opinion in Lipidology