Epigenetics of personality traits: an illustrative study of identical twins discordant for risk-taking behavior

Individual differences in social homeostasis

The concept of “social homeostasis”, introduced by Matthews and Tye in 2019, has provided a framework with which to consider our changing individual needs for social interaction, and the neurobiology underlying this system. This model was conceived as including detector systems, a control center with a setpoint, and effectors which allow us to seek out or avoid additional social contact. In this article, we review and theorize about the many different factors that might contribute to the setpoint of a person or animal, including individual, social, cultural, and other environmental factors. We conclude with a consideration of the empirical challenges of this exciting new model.

DNA methylation and waist-to-hip ratio: an epigenome-wide association study in Chinese monozygotic twins

PURPOSE

Epigenetic signatures such as DNA methylation may be associated with specific obesity traits. We performed an epigenome-wide association study (EWAS) by combining with the waist-to-hip ratio (WHR)-discordant monozygotic (MZ) twin design in an attempt to identify genetically independent DNA methylation marks associated with abdominal obesity in Northern Han Chinese and to determine the causation underlying.

METHODS

A total of 60 WHR discordant MZ twin pairs were selected from the Qingdao Twin Registry, China. Generalized estimated equation (GEE) model was used to regress the methylation level of CpG sites on WHR. The Inference about Causation through Examination of FAmiliaL CONfounding (ICE FALCON) was used to assess the temporal relationship between methylation and WHR. Gene expression analysis was conducted to validate the results of differentially methylated analyses.

RESULTS

EWAS identified 92 CpG sites with the level of P < 10^- 4 which were annotated to 32 genes, especially CADPS2, TUSC5, ZCCHC14, CORO7, COL23A1, CACNA1C, CYP26B1, and BCAT1. ICE FALCON showed significant causality between DNA methylation of several genes and WHR (P < 0.05). In region-based analysis, 14 differentially methylated regions (DMRs) located at 15 genes (slk-corrected P < 0.05) were detected. The gene expression analysis identified the significant correlation between expression levels of 5 differentially methylated genes and WHR (P < 0.05).

CONCLUSIONS

Our study identifies the associations between specific epigenetic variations and WHR in Northern Han Chinese. These DNA methylation signatures may have value as diagnostic biomarkers and provide novel insights into the molecular mechanisms of pathogenesis.

Evaluation of the stability of the palatal rugae using the three-dimensional superimposition technique following orthodontic treatment

OBJECTIVES

To determine the uniqueness and stability of the palatal rugae after orthodontic treatment.

METHODS

Cast models of untreated subjects (n=50) were obtained twice at intervals of 8-30 months. Cast models of patients who received non-extraction (n=50) and extraction (n=50) orthodontic treatment were obtained before and after treatment at intervals of 11-41 months and 14-49 months, respectively. All 300 cast models were scanned digitally. The palatal rugae were manually extracted and transformed into 3D point clouds using reverse engineering software. An iterative closest point (ICP) registration algorithm based on correntropy was applied, and the minimum point-to-point root mean square (RMS) distances were calculated to analyze the deviation of palatal rugae for scans of the same subject (intrasubject deviation [ISD]) and between different subjects (between-subject deviation [BSD]). Differences in ISD between each group and the deviation between ISD and BSD of all 150 subjects were evaluated.

RESULTS

Significant differences were found in the 150 ISD and 1225 BSD in each group, as well as the 150 ISD and 11175 BSD across all groups. The mean values of ISD in untreated, non-extraction and extraction group were 0.178, 0.229 and 0.333 mm, respectively. When the first ruga was excluded in the extraction group, the mean ISD decreased to 0.241 mm, which was not significantly different from that in the non-extraction group (p=0.314).

CONCLUSIONS

Orthodontic treatment can influence the palatal rugae, especially in cases of extraction. Furthermore, variation mainly existed in the first ruga in cases of extraction. However, palatal rugae are still unique and may be used as a supplementary tool for individual identification.

CLINICAL SIGNIFICANCE

This study indicates that palatal rugae might be applied in the evaluation of orthodontic tooth movement and forensic individual identification. The registration algorithm based on correntropy provides a credible, precise, and convenient method for palatal rugae superimposition.

An investigation into DNA methylation patterns associated with risk preference in older individuals

Risk preference is a complex trait governed by psycho-social, environmental and genetic determinants. We aimed to examine how an individual’s risk preference associates with their epigenetic profile.

Risk preferences were ascertained by asking participants of the Northern Ireland COhort for the Longitudinal study of Ageing to make a series of choices between hypothetical income scenarios. From these, four risk preference categories were derived, ranging from risk-averse to risk-seeking. Illumina’s Infinium High-Density Methylation Assay was used to evaluate the status of 862,927 CpGs.

Risk preference and DNA methylation data were obtained for 1,656 individuals. The distribution of single-site DNA methylation levels between risk-averse and risk-seeking individuals was assessed whilst adjusting for age, sex and peripheral white cell counts. In this discovery cohort, 55 CpGs were identified with significantly different levels of methylation (p≤x10⁻⁵) between risk-averse and risk-seeking individuals when adjusting for the maximum number of covariates. No CpGs were significantly differentially methylated in any of the risk preference groups at an epigenome-wide association level (p<9x10⁻⁸) following covariate adjustment.

Protein-coding genes NWD1 and LRP1 were among the genes in which the top-ranked dmCpGs were located for all analyses conducted. Mutations in these genes have previously been linked to neurological conditions.

Epigenetic modifications have not previously been linked to risk-aversion using a population cohort, but may represent important biomarkers of accumulated, complex determinants of this trait. Several striking results from this study support further analysis of DNA methylation as an important link between measurable biomarkers and health behaviours.

Integrating the study of personality and psychopathology in the context of gene-environment correlations across development

OBJECTIVE

A key principle of individual differences research is that biological and environmental factors jointly influence personality and psychopathology. Genes and environments interact to influence the emergence and stability of both normal and abnormal behavior (i.e., genetic predisposition, X, is exacerbated or buffered under environmental conditions, Y, or vice versa), including by shaping the neural circuits underpinning behavior. The interplay of genes and environments is also reflected in various ways in which they are correlated (i.e., rGE). That is, the same genetic factors that give rise to personality or psychopathology also shape that person's environment.

METHODS

In this review, we outline passive, evocative, and active rGE processes and review the findings of studies that have addressed rGE in relation to understanding individual differences in personality and psychopathology across development.

RESULTS

Throughout, we evaluate the question of whether it is possible, not only to differentiate the person from their problems, but also to differentiate the person from their problems and their environment.

CONCLUSIONS

We provide recommendations for future research to model rGE and better inform our ability to study personality and psychopathology, while separating the influence of the environment.

Methylome and transcriptome profiling in Myasthenia Gravis monozygotic twins

OBJECTIVE

To identify novel genetic and epigenetic factors associated with Myasthenia gravis (MG) using an identical twins experimental study design.

METHODS

The transcriptome and methylome of peripheral monocytes were compared between monozygotic (MZ) twins discordant and concordant for MG, as well as with MG singletons and healthy controls, all females. Sets of differentially expressed genes and differentially methylated CpGs were validated using RT-PCR for expression and target bisulfite sequencing for methylation on additional samples.

RESULTS

>100 differentially expressed genes and ∼1800 differentially methylated CpGs were detected in peripheral monocytes between MG patients and controls. Several transcripts associated with immune homeostasis and inflammation resolution were reduced in MG patients. Only a relatively few genes differed between the discordant healthy and MG co-twins, and both their expression and methylation profiles demonstrated very high similarity.

INTERPRETATION

This is the first study to characterize the DNA methylation profile in MG, and the expression profile of immune cells in MZ twins with MG. Results suggest that numerous small changes in gene expression or methylation might together contribute to disease. Impaired monocyte function in MG and decreased expression of genes associated with inflammation resolution could contribute to the chronicity of the disease. Findings may serve as potential new predictive biomarkers for disease and disease activity, as well as potential future targets for therapy development. The high similarity between the healthy and the MG discordant twins, suggests that a molecular signature might precede a clinical phenotype, and that genetic predisposition may have a stronger contribution to disease than previously assumed.

Differentially Methylated DNA Regions in Monozygotic Twin Pairs Discordant for Rheumatoid Arthritis: An Epigenome-Wide Study

Objectives

In an explorative epigenome-wide association study (EWAS) to search for gene independent, differentially methylated DNA positions and regions (DMRs) associated with rheumatoid arthritis (RA) by studying monozygotic (MZ) twin pairs discordant for RA.

Methods

Genomic DNA was isolated from whole blood samples from 28 MZ twin pairs discordant for RA. DNA methylation was measured using the HumanMethylation450 BeadChips. Smoking, anti-cyclic citrullinated peptide antibodies, and immunosuppressive treatment were included as covariates. Pathway analysis was performed using GREAT.

Results

Smoking was significantly associated with hypomethylation of a DMR overlapping the promoter region of the RNF5 and the AGPAT1, which are implicated in inflammation and autoimmunity, whereas DMARD treatment induced hypermethylation of the same region. Additionally, the promotor region of both S100A6 and EFCAB4B were hypomethylated, and both genes have previously been associated with RA. We replicated several candidate genes identified in a previous EWAS in treatment-naïve RA singletons. Gene-set analysis indicated the involvement of immunologic signatures and cancer-related pathways in RA.

Conclusion

We identified several differentially methylated regions associated with RA, which may represent environmental effects or consequences of the disease and plausible biological pathways pertinent to the pathogenesis of RA.

Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation

Personality traits are heritable and respond to natural selection, but are at the same time influenced by the ontogenetic environment. Epigenetic effects, such as DNA methylation, have been proposed as a key mechanism to control personality variation. However, to date little is known about the contribution of epigenetic effects to natural variation in behaviour. Here, we show that great tit (Parus major) lines artificially selected for divergent exploratory behaviour for four generations differ in their DNA methylation levels at the dopamine receptor D4 (DRD4) gene. This D4 receptor is statistically associated with personality traits in both humans and nonhuman animals, including the great tit. Previous work in this songbird failed to detect functional genetic polymorphisms within DRD4 that could account for the gene-trait association. However, our observation supports the idea that DRD4 is functionally involved in exploratory behaviour but that its effects are mediated by DNA methylation. While the exact mechanism underlying the transgenerational consistency of DRD4 methylation remains to be elucidated, this study shows that epigenetic mechanisms are involved in shaping natural variation in personality traits. We outline how this first finding provides a basis for investigating the epigenetic contribution to personality traits in natural systems and its subsequent role for understanding the ecology and evolution of behavioural consistency.

Twin methodology in epigenetic studies

Since the final decades of the last century, twin studies have made a remarkable contribution to the genetics of human complex traits and diseases. With the recent rapid development in modern biotechnology of high-throughput genetic and genomic analyses, twin modelling is expanding from analysis of diseases to molecular phenotypes in functional genomics especially in epigenetics, a thriving field of research that concerns the environmental regulation of gene expression through DNA methylation, histone modification, microRNA and long non-coding RNA expression, etc. The application of the twin method to molecular phenotypes offers new opportunities to study the genetic (nature) and environmental (nurture) contributions to epigenetic regulation of gene activity during developmental, ageing and disease processes. Besides the classical twin model, the case co-twin design using identical twins discordant for a trait or disease is becoming a popular and powerful design for epigenome-wide association study in linking environmental exposure to differential epigenetic regulation and to disease status while controlling for individual genetic make-up. It can be expected that novel uses of twin methods in epigenetic studies are going to help with efficiently unravelling the genetic and environmental basis of epigenomics in human complex diseases.

Genome-wide DNA methylation variability in adolescent monozygotic twins followed since birth

DNA methylation patterns are characterized by highly conserved developmental programs, but allow for divergent gene expression resulting from stochastic epigenetic drift or divergent environments. Genome-wide methylation studies in monozygotic (MZ) twins are providing insight into the extent of epigenetic variation that occurs, irrespective of genotype. However, little is known about the variability of DNA methylation patterns in adolescence, a period involving significant and rapid physical, emotional, social, and neurodevelopmental change. Here, we assessed genome-wide DNA methylation using the 450 K Illumina BeadChip in a sample of 37 MZ twin pairs followed longitudinally since birth to investigate: 1) the extent of variation in DNA methylation in identical genetic backgrounds in adolescence and; 2) whether these variations are randomly distributed or enriched in particular functional pathways. We also assessed stability of DNA methylation over 3-6 months to distinguish stable trait-like and variable state-like genes. A pathway analysis found high within-pair variability in genes associated with development, cellular mechanisms, tissue and cell morphology, and various disorders. Test-retest analyses performed in a sub-sample of 8 twin pairs demonstrated enrichment in gene pathways involved in organismal development, cellular growth and proliferation, cell signaling, and particular disorders. The variability found in functional gene pathways may plausibly underlie phenotypic differences in this adolescent MZ twin sample. Furthermore, we assessed stability of methylation over 3-6 months and found that some genes were stable while others were unstable, suggesting that the methylome remains dynamic in adolescence and that dynamic sites tend to be organized in certain gene pathways.

Power and sample size estimation for epigenome-wide association scans to detect differential DNA methylation

BACKGROUND

Epigenome-wide association scans (EWAS) are under way for many complex human traits, but EWAS power has not been fully assessed. We investigate power of EWAS to detect differential methylation using case-control and disease-discordant monozygotic (MZ) twin designs with genome-wide DNA methylation arrays.

METHODS AND RESULTS

We performed simulations to estimate power under the case-control and discordant MZ twin EWAS study designs, under a range of epigenetic risk effect sizes and conditions. For example, to detect a 10% mean methylation difference between affected and unaffected subjects at a genome-wide significance threshold of P = 1 × 10^-6, 98 MZ twin pairs were required to reach 80% EWAS power, and 112 cases and 112 controls pairs were needed in the case-control design. We also estimated the minimum sample size required to reach 80% EWAS power under both study designs. Our analyses highlighted several factors that significantly influenced EWAS power, including sample size, epigenetic risk effect size, the variance of DNA methylation at the locus of interest and the correlation in DNA methylation patterns within the twin sample.

CONCLUSIONS

We provide power estimates for array-based DNA methylation EWAS under case-control and disease-discordant MZ twin designs, and explore multiple factors that impact on EWAS power. Our results can help guide EWAS experimental design and interpretation for future epigenetic studies.

Epigenetics of discordant monozygotic twins: implications for disease

Monozygotic (MZ) twins share nearly all of their genetic variants and many similar environments before and after birth. However, they can also show phenotypic discordance for a wide range of traits. Differences at the epigenetic level may account for such discordances. It is well established that epigenetic states can contribute to phenotypic variation, including disease. Epigenetic states are dynamic and potentially reversible marks involved in gene regulation, which can be influenced by genetics, environment, and stochastic events. Here, we review advances in epigenetic studies of discordant MZ twins, focusing on disease. The study of epigenetics and disease using discordant MZ twins offers the opportunity to control for many potential confounders encountered in general population studies, such as differences in genetic background, early-life environmental exposure, age, gender, and cohort effects. Recently, analysis of disease-discordant MZ twins has been successfully used to study epigenetic mechanisms in aging, cancer, autoimmune disease, psychiatric, neurological, and multiple other traits. Epigenetic aberrations have been found in a range of phenotypes, and challenges have been identified, including sampling time, tissue specificity, validation, and replication. The results have relevance for personalized medicine approaches, including the identification of prognostic, diagnostic, and therapeutic targets. The findings also help to identify epigenetic markers of environmental risk and molecular mechanisms involved in disease and disease progression, which have implications both for understanding disease and for future medical research.

Sexually selected traits: a fundamental framework for studies on behavioral epigenetics

Emerging evidence suggests that epigenetic-based mechanisms contribute to various aspects of sex differences in brain and behavior. The major obstacle in establishing and fully understanding this linkage is identifying the traits that are most susceptible to epigenetic modification. We have proposed that sexual selection provides a conceptual framework for identifying such traits. These are traits involved in intrasexual competition for mates and intersexual choice of mating partners and generally entail a combination of male-male competition and female choice. These behaviors are programmed during early embryonic and postnatal development, particularly during the transition from the juvenile to adult periods, by exposure of the brain to steroid hormones, including estradiol and testosterone. We evaluate the evidence that endocrine-disrupting compounds, including bisphenol A, can interfere with the vital epigenetic and gene expression pathways and with the elaboration of sexually selected traits with epigenetic mechanisms presumably governing the expression of these traits. Finally, we review the evidence to suggest that these steroid hormones can induce a variety of epigenetic changes in the brain, including the extent of DNA methylation, histone protein alterations, and even alterations of noncoding RNA, and that many of the changes differ between males and females. Although much previous attention has focused on primary sex differences in reproductive behaviors, such as male mounting and female lordosis, we outline why secondary sex differences related to competition and mate choice might also trace their origins back to steroid-induced epigenetic programming in disparate regions of the brain.

Using epigenome-wide association scans of DNA methylation in age-related complex human traits

With rapid technological advancements emerging epigenetic studies of complex traits have shifted from candidate gene analyses towards epigenome-wide association studies (EWAS). EWAS aim to systematically identify epigenetic variants across the genome that associate with complex phenotypes. Recent EWAS using case-control and disease-discordant identical twin designs have identified phenotype-associated differentially methylated regions for several traits. However, EWAS still face many challenges related to methodology, design and interpretation, owing to the dynamic nature of epigenetic variants over time. This article reviews analytical considerations in conducting EWAS and recent applications of this approach to human aging and age-related complex traits.

Maternal stress induces epigenetic signatures of psychiatric and neurological diseases in the offspring

The gestational state is a period of particular vulnerability to diseases that affect maternal and fetal health. Stress during gestation may represent a powerful influence on maternal mental health and offspring brain plasticity and development. Here we show that the fetal transcriptome, through microRNA (miRNA) regulation, responds to prenatal stress in association with epigenetic signatures of psychiatric and neurological diseases. Pregnant Long-Evans rats were assigned to stress from gestational days 12 to 18 while others served as handled controls. Gestational stress in the dam disrupted parturient maternal behaviour and was accompanied by characteristic brain miRNA profiles in the mother and her offspring, and altered transcriptomic brain profiles in the offspring. In the offspring brains, prenatal stress upregulated miR-103, which is involved in brain pathologies, and downregulated its potential gene target Ptplb. Prenatal stress downregulated miR-145, a marker of multiple sclerosis in humans. Prenatal stress also upregulated miR-323 and miR-98, which may alter inflammatory responses in the brain. Furthermore, prenatal stress upregulated miR-219, which targets the gene Dazap1. Both miR-219 and Dazap1 are putative markers of schizophrenia and bipolar affective disorder in humans. Offspring transcriptomic changes included genes related to development, axonal guidance and neuropathology. These findings indicate that prenatal stress modifies epigenetic signatures linked to disease during critical periods of fetal brain development. These observations provide a new mechanistic association between environmental and genetic risk factors in psychiatric and neurological disease.

Twins for epigenetic studies of human aging and development

Most of the complex traits including aging phenotypes are caused by the interaction between genome and environmental conditions and the interface of epigenetics may be a central mechanism. Although modern technologies allow us high-throughput profiling of epigenetic patterns already at genome level, our understanding of genetic and environmental influences on the epigenetic processes remains limited. Twins are of special interest for genetic studies due to their genetic similarity and rearing-environment sharing. The classical twin design has made a great contribution in dissecting the genetic and environmental contributions to human diseases and complex traits. In the era of functional genomics, the valuable sample of twins is helping to bridge the gap between gene activity and the environments through epigenetic mechanisms unlimited by DNA sequence variations. We propose to extend the classical twin design to study the aging-related molecular epigenetic phenotypes and link them with environmental exposures especially early life events. Different study designs and application issues will be highlighted and novel approaches introduced with aim at making uses of twins in assessing the environmental impact on epigenetic changes during development and in the aging process.

DNA methylation studies using twins: what are they telling us?

Recent studies have identified both heritable DNA methylation effects and differential methylation in disease-discordant identical twins. Larger sample sizes, replication, genetic-epigenetic analyses and longitudinal assays are now needed to establish the role of epigenetic variants in disease.

Current perspectives on the neurobiology of drug addiction: a focus on genetics and factors regulating gene expression

Drug addiction is a chronic, relapsing disorder defined by cyclic patterns of compulsive drug seeking and taking interspersed with episodes of abstinence. While genetic variability may increase the risk of addictive behaviours in an individual, exposure to a drug results in neuroadaptations in interconnected brain circuits which, in susceptible individuals, are believed to underlie the transition to, and maintenance of, an addicted state. These adaptations can occur at the cellular, molecular, or (epi)genetic level and are associated with synaptic plasticity and altered gene expression, the latter being mediated via both factors affecting translation (epigenetics) and transcription (non coding microRNAs) of the DNA or RNA itself. New advances using techniques such as optogenetics have the potential to increase our understanding of the microcircuitry mediating addictive behaviours. However, the processes leading to addiction are complex and multifactorial and thus we face a major contemporary challenge to elucidate the factors implicated in the development and maintenance of an addicted state.

Genetic and environmental influences on nutrient intake

The relationship between genetic and the environment represents a pathway to better understand individual variations in nutrition intake and food preferences. However, the present literature is weakened somewhat by methodological flaws (e.g., overreliance on self-report questionnaires), discrepancies in statistical approaches, and inconsistent findings. Little research on this topic to date has included examination of micronutrient intake. The purpose of this study is to improve the existing literature on genetic and environmental influences on energy and nutrient intake by addressing these gaps. Twin pairs (N = 358; age 11-13 years) provided 3-day food intake diaries, which were assessed for intake of total energy, macronutrients, and micronutrients. Structural equation modeling revealed that genetic influences accounted for a significant portion of the total variance in total energy (48 %), macronutrients (35-45 %), minerals (45 %), and vitamins (21 %). Consistent with previous studies, the shared environment appeared to contribute little to nutritional intake. Findings on vitamin and mineral intake are novel and are particularly beneficial for further research on the contribution of micronutrients to individual physical health status. Better understanding of the linkage between genes, environment, and nutritional intake and deficiencies can clarify behavioral and physical outcomes, potentially informing risk reduction, primary prevention, and intervention strategies.

Genetic, environmental and stochastic factors in monozygotic twin discordance with a focus on epigenetic differences

Genetic-epidemiological studies on monozygotic (MZ) twins have been used for decades to tease out the relative contributions of genes and the environment to a trait. Phenotypic discordance in MZ twins has traditionally been ascribed to non-shared environmental factors acting after birth, however recent data indicate that this explanation is far too simple. In this paper, we review other reasons for discordance, including differences in the in utero environment, genetic mosaicism, and stochastic factors, focusing particularly on epigenetic discordance. Epigenetic differences are gaining increasing recognition. Although it is clear that in specific cases epigenetic alterations provide a causal factor in disease etiology, the overall significance of epigenetics in twin discordance remains unclear. It is also challenging to determine the causality and relative contributions of environmental, genetic, and stochastic factors to epigenetic variability. Epigenomic profiling studies have recently shed more light on the dynamics of temporal methylation change and methylome heritability, yet have not given a definite answer regarding their relevance to disease, because of limitations in establishing causality. Here, we explore the subject of epigenetics as another component in human phenotypic variability and its links to disease focusing particularly on evidence from MZ twin studies.

Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships

Changes in epigenetic marks such as DNA methylation and histone acetylation are associated with a broad range of disease traits, including cancer, asthma, metabolic disorders, and various reproductive conditions. It seems plausible that changes in epigenetic state may be induced by environmental exposures such as malnutrition, tobacco smoke, air pollutants, metals, organic chemicals, other sources of oxidative stress, and the microbiome, particularly if the exposure occurs during key periods of development. Thus, epigenetic changes could represent an important pathway by which environmental factors influence disease risks, both within individuals and across generations. We discuss some of the challenges in studying epigenetic mediation of pathogenesis and describe some unique opportunities for exploring these phenomena.

Monozygotic Twins With Neurofibromatosis Type 1 (NF1) Display Differences in Methylation ofNF1Gene Promoter Elements, 5' Untranslated region, Exon and Intron 1

Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder caused by heterozygotic inactivation of the NF1 tumor suppressor gene at 17q11.2. The associated phenotypes are highly variable, and modifying genes have been proposed to explain at least in part the intriguing expressivity. Given that haploinsufficiency of the NF1 gene product neurofibromin is responsible for some of the clinical manifestations, variations in expression of the wildtype NF1 allele might modify the phenotype. We therefore investigated epigenetic molecular modifications that could result in variable expression of the normal NF1 allele. To exclude confounding by DNA sequence variations, we analyzed monozygotic twin pairs with NF1 who presented with several discordant features. We fine-mapped the methylation pattern of a nearly 1 kb NF1 promoter region in lymphocytes of 8 twin pairs. All twin pairs showed significant intra-pair differences in methylation, especially of specific promoter subregions such as 5'UTR, exon 1 and intron 1 (+7 to +622), transcription factor binding sites and promoter elements like NF1HCS. Furthermore, we detected significant intra-pair differences in cytosine methylation for the region from -249 to -234 with regard to discordance for optic glioma with a higher grade of methylation in glioma cases. In conclusion, our findings of epigenetic differences of the NF1 promoter in leukocytes within mono zygotic twin pairs may serve as a proof of principle for other tissues. The results point towards a role of methylation patterns of the normal NF1 allele for expression differences and for modification of the NF1 phenotype.

Epigenetic programming of neurodegenerative diseases by an adverse environment

Experience and environment can critically influence the risk and progression of neurodegenerative disorders. Epigenetic mechanisms, such as miRNA expression, DNA methylation, and histone modifications, readily respond to experience and environmental factors. Here we propose that epigenetic regulation of gene expression and environmental modulation thereof may play a key role in the onset and course of common neurological conditions, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and multiple sclerosis. For example, epigenetic mechanisms may mediate long-term responses to adverse experience, such as stress, to affect disease susceptibility and the course of neurodegenerative events. This review introduces the epigenetic components and their possible role in mediating neuropathological processes in response to stress. We argue that epigenetic modifications will affect neurodegenerative events through altered gene function. The study of epigenetic states in neurodegenerative diseases presents an opportunity to gain new insights into risk factors and pathogenic mechanisms. Moreover, research into epigenetic regulation of disease may revolutionize health care by opening new avenues of personalized, preventive and curative medicine.

The value of twins in epigenetic epidemiology

During past decades, twin studies have played an important role in genetic epidemiology studies of complex traits. The strength of twin studies lies in the ability to disentangle genetic and environmental factors that contribute to a phenotype, by comparing genetically identical monozygotic twins to dizygotic twins, who share on average 50% of genetic variants. Twin studies now offer the opportunity to study epigenetic variation across the genome with two aims. First, twin studies can improve our understanding of the factors regulating epigenetic variability by assessing the heritability of epigenetic variants. Secondly, the use of twins in epigenetic research is increasingly recognized as an important approach to help unravel the complexities associated with human development and disease. The strategic use of identical twins discordant for complex disease has revealed the importance of linking epigenetic disruption to the disease-associated risk in humans. Lastly, we also discuss the possibility that epigenetic effects on disease may in part explain some of the missing heritability in genome-wide association studies. The study of human epigenetic factors in twins can inform the role of genetics, as well as in utero and postnatal environments to the establishment, maintenance and functional consequences of human epigenome variation.

Why are monozygotic twins different?

Although popularly designated as "identical", monozygotic (MZ) twins are rarely identical. Much has been speculated on the origin of MZ twins and several theories have been proposed. Post-fertilization events, such as chromosomal mosaicism, skewed X-inactivation and imprinting mechanisms, as well as other epigenetic mechanisms are responsible for the differences between MZ twins. Numerous discordant MZ twins have been reported including discordance for lateral asymmetry, major malformation, growth and intrauterine death of the co-twin. This discrepancy may have long-term implications on complex diseases and their predisposition, organ transplantation and interpretation of twin-based studies. We reviewed the genotypic and phenotypic differences between MZ twins and discuss their main causes.

A twin approach to unraveling epigenetics

The regulation of gene expression plays a pivotal role in complex phenotypes, and epigenetic mechanisms such as DNA methylation are essential to this process. The availability of next-generation sequencing technologies allows us to study epigenetic variation at an unprecedented level of resolution. Even so, our understanding of the underlying sources of epigenetic variability remains limited. Twin studies have played an essential role in estimating phenotypic heritability, and these now offer an opportunity to study epigenetic variation as a dynamic quantitative trait. High monozygotic twin discordance rates for common diseases suggest that unexplained environmental or epigenetic factors could be involved. Recent genome-wide epigenetic studies in disease-discordant monozygotic twins emphasize the power of this design to successfully identify epigenetic changes associated with complex traits. We describe how large-scale epigenetic studies of twins can improve our understanding of how genetic, environmental and stochastic factors impact upon epigenetics, and how such studies can provide a comprehensive understanding of how epigenetic variation affects complex traits.

Epigenetic mechanisms in cancer

After the completion of the human genome, a need was identified by scientists to look for a functional map of the human genome. Epigenomics provided functional characteristics of genes identified in the genome. Epigenetics is the alteration in gene expression (function) without changing the nucleotide sequence. Both activation and inactivation of cancer-associated genes can occur by epigenetic mechanisms. The major players in epigenetic mechanisms of gene regulation are DNA methylation, histone deacetylation, chromatin remodeling, small noncoding RNA expression and gene imprinting. In the last few years, epigenetic mechanisms have been studied in a number of tumor types and epigenetic markers have been identified that are suitable for cancer detection, diagnosis, follow-up of treatment and screening high-risk populations. One interesting aspect of epigenetics is the reactivation of genes by successful reversion of some epigenetic changes using chemicals. The reversibility of epigenetic aberrations has made them attractive targets for cancer treatment with modulators that demethylate DNA and inhibit histone deacetylases, leading to the reactivation of silenced genes. In this article, we have described the current status of this powerful science and discussed the challenges in the clinical fields where epigenetic approaches in cancer are applied.

Dissecting complex phenotypes using the genomics of twins

Genetics in the post-genomic period is shifting from structural to functional genetics or genomics. Meanwhile, the use of twins is largely expanding from traditional heritability estimation for disease phenotypes to the study of both diseases and various molecular phenotypes, such as the regulatory phenotypes in functional genomics concerning gene expression and regulation, by engaging both classical twin design and marker-based gene mapping techniques in genetic epidemiology. New research designs have been proposed for making novel uses of twins in studying the molecular basis in the epigenetics of human diseases. Besides, twins not only serve as ideal samples for disease gene mapping using conventional genetic markers but also represent an excellent model for associating DNA copy number variations, a structural genetic marker, with human diseases. It is believed that, with the rapid development in biotechniques and new advances in bioinformatics, the unique samples of twins will make new contributions to our understanding of the nature and nurture in complex disease development and in human health. This paper aims at summarizing the new uses of twins in current genetic studies and suggesting novel proposes together with useful design and analytical strategies.

Genetic influence on human intelligence (Spearman's g): how much?

The history and conceptual background of the heritability statistic is briefly discussed. The construct of heritability is embedded in the method of structural equation modeling widely used in modern population genetics and in human behavior genetics. The application of structural equation modeling to behavioral phenotypes is shown to be a useful and informative analytic tool, as it implements the research strategy of 'strong inference'. I describe the application of 'strong inference', via the use of structural equation models in the domain of human intelligence, and demonstrate its utility as a means of refuting well formulated scientific hypotheses. The construct of Spearman's g is shown to be a strongly confirmed scientific hypothesis. Genetic and environmental influences are shown to influence g differentially over time, with shared environmental influences predominating early in life, but dissipating to near zero by adulthood. The hypothesis of substantively significant genetic influence on adult g is documented by multiple lines of evidence and numerous replications.

Epigenetic modifications in rheumatoid arthritis

Over the last decades, genetic factors for rheumatoid diseases like the HLA haplotypes have been studied extensively. However, during the past years of research, it has become more and more evident that the influence of epigenetic processes on the development of rheumatic diseases is probably as strong as the genetic background of a patient. Epigenetic processes are heritable changes in gene expression without alteration of the nucleotide sequence. Such modifications include chromatin methylation and post-translational modification of histones or other chromatin-associated proteins. The latter comprise the addition of methyl, acetyl, and phosphoryl groups or even larger moieties such as binding of ubiquitin or small ubiquitin-like modifier. The combinatory nature of these processes forms a complex network of epigenetic modifications that regulate gene expression through activation or silencing of genes. This review provides insight into the role of epigenetic alterations in the pathogenesis of rheumatoid arthritis and points out how a better understanding of such mechanisms may lead to novel therapeutic strategies.