Article Published in the Author Account of

Richard Chahwan

The Multidimensional Nature of Epigenetic Information and Its Role in Disease

Abstract: This year marks the 10th anniversary of the publications that reported the initial human genome sequence. In the historic press conference that announced this landmark accomplishment, it was proclaimed that the genome sequence would "revolutionize the diagnosis, prevention, and treatment of most, if not all, human diseases." However, subsequent work over the past decade has revealed that "complex diseases" are much more intricate than originally thought. Even with the advent of several new powerful technologies, our understanding of the underlying genetic etiologies of most complex and non-Mendelian diseases is far from complete. These results have raised the possibility that the DNA sequence, i.e., genetic information, may not be the only relevant source of information in order to understand the molecular basis of disease. In this review, we assemble evidence that information encoded beyond the DNA sequence, i.e., epigenetic information, may hold the key to a better understanding of various pathological conditions. Unlike the genetic information encoded within the DNA sequence, epigenetic information can be stored in multiple dimensions, such as in the form of DNA modifications, RNA, or protein. Ideas presented here support the view that to better understand the molecular etiology of diseases, we need to gain a better understanding of both the genetic and epigenetic components of biological information. We hence believe that the fast development of genome-wide technologies will facilitate a better understanding of both genetic and epigenetic dimensions of disease.



The Duality of Biological Information: Genetic and Epigenetic

In this era of molecular medicine, understanding the duality of biological information, namely genetic and epigenetic, is becoming increasingly important for the prevention, diagnosis, and treatment of diseases. Beyond the essential focus on physical examination and observation of patients, medicine experienced a revolution after the identification of DNA as the heritable material and the source of genetic information. The central dogma of biology, which was first postulated by Francis Crick in 1958 (Crick, 1958), has provided an intellectual framework for such a revolution (inner circle in Figure 1). The sequential transfer of information from DNA to RNA and then to protein described by the central dogma has helped us understand that mutations in DNA (i.e., genetic variation) can have an irreversible deleterious impact on protein function that can result in disease (Lander, 2011). The international effort that resulted in the sequencing of the entire human genome has further enhanced our understanding of classical genetic diseases. Yet additional approaches are still needed to help us understand the nature of non-Mendelian and complex diseases, which are likely to be caused by a combination of genetic and epigenetic abnormalities (Ptak and Petronis, 2008). This idea is further supported by the appearance of epigenetic differences, manifested in distinct traits and disease susceptibilities, during the lifetime of monozygotic twins (Fraga et al., 2005).

Figure 1. The multiple dimensions of biological information. The dualism of biological information (i.e., genetic and epigenetic) is depicted here in the form of two concentric circles. The flow of genetic information from DNA to RNA and then to protein, which was postulated by the central dogma of molecular biology, is projected in the center of the figure. Beyond the genetic foundation, epigenetics is an essential corequisite to fully understand biological phenotypes. Thus, the outermost circle encompasses different epigenetic elements, including widely accepted ones (e.g., methyl-cytosine, histone modifications, chromatin remodeling), emerging elements (e.g., hydroxymethyl-cytosine, regulatory and edited RNAs, prions), and even elements still unexplored (e.g., cellular structures). In the periphery, the figure delineates phenotypes that show how relevant is the regulation of the epigenetic information to prevent disease. The ultimate challenge for molecular medicine is to better understand the complex relationship between genetic and epigenetic spheres, in an effort to improve prevention, diagnosis, and treatment of human disease.

Figure 1. The multiple dimensions of biological information. The dualism of biological information (i.e., genetic and epigenetic) is depicted here in the form of two concentric circles. The flow of genetic information from DNA to RNA and then to protein, which was postulated by the central dogma of molecular biology, is projected in the center of the figure. Beyond the genetic foundation, epigenetics is an essential corequisite to fully understand biological phenotypes. Thus, the outermost circle encompasses different epigenetic elements, including widely accepted ones (e.g., methyl-cytosine, histone modifications, chromatin remodeling), emerging elements (e.g., hydroxymethyl-cytosine, regulatory and edited RNAs, prions), and even elements still unexplored (e.g., cellular structures). In the periphery, the figure delineates phenotypes that show how relevant is the regulation of the epigenetic information to prevent disease. The ultimate challenge for molecular medicine is to better understand the complex relationship between genetic and epigenetic spheres, in an effort to improve prevention, diagnosis, and treatment of human disease.

Numerous phenomena have been described where the transmission of phenotypes occurred without any underlying changes in the DNA sequence (i.e., epigenetic variation). Ever since C.H. Waddington first coined the term epigenetics in 1942 (Waddington, 1942), its definition has slowly evolved over time. An accepted modern definition of epigenetics is described by Arthur Riggs and colleagues as “the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence” (Russo et al., 1996). Work from numerous labs is helping to rapidly uncover the multiple dimensions of epigenetic information and their roles in promoting disease (Figure 1).

Theoretically, the transmission of epigenetic information might be mediated by any macromolecule present within a cell, including DNA (beyond its sequence), RNA, protein, lipids, or sugars. Current evidence seems to support that this is true at least for the first three of these macromolecules (discussed below and Figure 1). However, very little is known about the epigenetic potential, if any, of lipids (Lund and Zaina, 2007; Saddoughi et al., 2008) or sugars (Lauc and Zoldos, 2010). In addition, molecular cellular structures such as organelles and the cellular membrane have been postulated to possess an ability to mediate structural inheritance through an as yet unknown mechanism (Beisson and Sonneborn, 1965; Preer, 2006). It would be intriguing if these additional cellular elements may emerge in the future as additional media for the storage and transmission of epigenetic information (Figure 1, right section) and whether they could ultimately be implicated in human pathologies.

Given the variety of sources that can encode epigenetic information, we hereby discuss that unlike the uni-dimensional nature of genetic DNA mutations, aberration in epigenetic information could be multidimensional in scope, potentially offering a better understanding of non-Mendelian and complex diseases. The emerging availability of genome-wide high-throughput sequencing technologies combined with the plasticity and reversibility of epigenetic information highlight the intriguing translational potential of understanding the connection between epigenetic deregulation and disease.

DNA: The First Epigenetic Dimension

Modifying DNA without mutating the underlying sequence

DNA is a stable storage form for genetic information (Figure 1). Despite this stability, DNA molecules may still be chemically modified. Many times, such modifications can seriously damage DNA and activate a variety of DNA repair mechanisms to prevent the accumulation of mutations. Spontaneous or mutagen-induced DNA modifications that may be deleterious usually include oxidation of bases, conversion of amine groups to diazo groups, formation of covalent adducts, deamination of cytosines or adenines, loss of purine bases to form apurinic sites, or generation of strand breaks. In a distinct group of modifications, DNA methylation can occur at cytosines, mostly within CpG dinucleotides in vertebrates (Bird, 2002), but as opposed to the aforementioned deleterious alterations, this covalent modification of DNA does not trigger repair mechanisms. The methyl group can be stably transmitted to daughter cells after cell division and can influence the binding of sequence-specific and methyl-binding proteins, ultimately affecting gene expression (Law and Jacobsen, 2010). In fact, DNA methylation is essential for normal development and is associated with parental imprinting (Reik and Walter, 2001), inactivation of the X-chromosome (Wolf and Migeon, 1982), some of the phenotypic differences during aging (Rodriguez-Rodero et al., 2010), and several human pathologies (discussed below and Figure 1). Very recently, a family of enzymes, called TET proteins, has been shown to be able to oxidize 5-methylcytosines (5mC) to 5-hydroxymethylcytosine (5hmC) (Ito et al., 2010; Ko et al., 2010; Tahiliani et al., 2009). The function of 5hmC and its effects on gene expression are not known yet, but 5hmC has been found in multiple mammalian tissues (Globisch et al., 2010; Szwagierczak et al., 2010) and is speculated that it might play a role in epigenetic regulation (Kriaucionis and Heintz, 2009; Tahiliani et al., 2009).

Regulation of DNA methylation and disease

Although it has been postulated that there are mechanisms to “erase” 5mC, DNA methylation is a stable epigenetic mark that is difficult to remove and very little is known about enzymatic activities involved in active DNA demethylation in mammals (Law and Jacobsen, 2010; Wu and Zhang, 2010; Zhu, 2009). Several groups have recently suggested that the AID/APOBEC family of cytosine deaminases could deaminate 5mC and trigger DNA repair mechanisms to restore the unmethylated cytosine (Bhutani et al., 2009; Morgan et al., 2004; Popp et al., 2010; Rai et al., 2008). It is therefore plausible that the fine regulation of such deamination-mediated demethylation (D-demethylation) plays a role in local or global DNA demethylation, but could also have deleterious consequences pushing the epigenetic remodeling and the changes in gene expression towards malignancy and disease (Chahwan et al., 2010).

The importance of regulating epigenetic information in the form of methylated DNA is clearly demonstrated by disorders where the establishment, maintenance, or recognition of methylation marks is impaired. For example, abnormalities in the enzymes responsible for the establishment and maintenance of methylation patterns, referred to as DNA methyltransferases (DNMTs), have been associated with pathological conditions. Mutations in DNMT3B are associated with a rare Immunodeficiency-Centromere instability-Facial anomalies (ICF) syndrome, which is inherited as an autosomal recessive disorder (Ehrlich et al., 2008). In the absence of DNMT3B-mediated methylation, cells exhibit hypomethylation at various loci and aberrant chromosomal configurations, which have an impact on gene expression and the progression of the ICF syndrome (Kondo et al., 2000; Matarazzo et al., 2007). Another disorder, in this case caused by defects in the interpretation of the DNA methylation signal, is the X-linked dominant Rett syndrome. This neurodevelopmental disease is mainly caused by mutations in the MECP2 gene, which encodes a member of the family of proteins sharing a methyl-binding domain (MBD) (Amir et al., 1999). The loss of MECP2 functions results in deficiencies during the transduction of DNA methylation signals that deregulate gene expression patterns and the spatial organization of DNA into chromatin (Ballestar et al., 2005; Yasui et al., 2007).

DNA methylation and imprinting disorders

Distinct DNA methylation marks in either the female or the male germline are established before fertilization at specialized regulatory sequence elements, known as imprinting control regions (ICR). As a consequence, depending on the inheritance from either the mother or the father, parentally-dependent methylated ICRs will repress the allele-specific expression of certain neighboring imprinted genes that play important roles in the regulation of growth, development, and even behavior (Reik and Walter, 2001; Wan and Bartolomei, 2008). Methylation of CpG dinucleotides at imprinted regions can result in repression of gene expression by modulating the binding of transcription factors or insulator proteins, and also by inducing changes in chromatin structure that forms more compact DNA. The Prader-Willi, Angelman, Beckwith-Wiedemann, and Silver-Russel syndromes have been linked to imprinting disorders characterized by neurodevelopmental and growth abnormalities. In these diseases, genetic defects (i.e., deletions, duplications, uniparental disomies) or altered DNA methylation of specific ICRs abrogate imprinting and lead to an aberrant expression of the imprinted gene(s) (Falls et al., 1999). Other human diseases including autism, bipolar disorder, diabetes, familial hypertrophic cardiomyopathy, schizophrenia, and cancer have been related to the alteration of normal imprinting patterns (Falls et al., 1999; Jirtle, 1999; Morison and Reeve, 1998). Finally, some studies have suggested that epigenetic defects might accumulate at imprinted genes during assisted reproductive technologies, increasing the risk of imprinting disease syndromes (Lawrence and Moley, 2008).

DNA methylation and cancer

Despite the suggestion that there might be an epigenetic component involved in various diseases including autoimmune diseases (Meda et al., 2011), neurological disorders (Portela and Esteller, 2010), allergy (Pascual et al., 2010), and cardiovascular diseases (Ordovas and Smith, 2010), the study of cancer remains a paradigm for the study of epigenetic alterations in DNA methylation. In our current understanding of cancer, its heterogeneity reflects the complex functional interaction between oncogenes and tumor suppressor genes, which have been shown to harbor genetic aberrations that promote malignant transformation. In addition to this genetic component of cancer, the field has shown an increasing interest and comprehension of the importance of epigenetic aberrations in the initiation and progression of malignancies (Berdasco and Esteller, 2010; Feinberg and Tycko, 2004). For example, hypomethylation of DNA, which was the first epigenetic abnormality identified in cancer cells (Feinberg and Vogelstein, 1983a), might lead to (a) gene activation, promoting the overexpression of oncogenes such as RAS (Feinberg and Vogelstein, 1983b); (b) chromosomal instability, predisposing pericentromeric satellite sequences to break and translocate (e.g., Wilms tumors) (Qu et al., 1999), or allowing retrotransposable elements to “jump” (e.g., colorectal cancer) (Suter et al., 2004); and (c) acquire resistance to drugs, toxins, or viruses, through either promoting overexpression of multidrug-resistance genes (e.g., MDR1 gene in acute myelogenous leukemia) (Nakayama et al., 1998), deregulating methyltransferases (e.g., cadmium carcinogenesis) (Takiguchi et al., 2003), or activating latent viral genomes (e.g., Epstein-Barr virus in lymphomas) (Li and Minarovits, 2003).

On the other hand, hypermethylation of many tumor suppressor genes represents an important mechanism of gene silencing and is a hallmark of cancer (Esteller, 2002). Important cellular pathways might be sabotaged and deregulated by aberrant hypermethylation. For instance, various genes associated with cell cycle progression (e.g., CDKN2/p16/MTS1, a cyclin-dependent kinase inhibitor) (Herman et al., 1995), DNA repair (e.g., MLH1, which is involved in mismatch repair) (Herman and Baylin, 2003), cellular adhesion (e.g., CDH1, E-cadherin) (Grady et al., 2000), cell survival (e.g., DAPK1, death-associated protein kinase 1) (Katzenellenbogen et al., 1999), transcription factors (e.g., GATA4, zinc-finger transcription factor) (Akiyama et al., 2003), or receptor-mediated signaling pathways (e.g., ESR1, estrogen-receptor 1) (Ottaviano et al., 1994) have been shown to be hypermethylated in tumor tissues.

RNA: The Second Epigenetic Dimension

The RNA world

Out of the three macromolecules, it could be argued that RNA has been historically viewed as the least important. However, numerous discoveries that have been made in recent years have invigorated renewed interest in this dynamic molecule, which could function as a key regulator of the epigenetic landscape (Bourc’his and Voinnet, 2010) (Figure 1). Although the idea that RNA can be a source of epigenetic information is not universally accepted, we discuss here several studies that support an epigenetic role for RNAs.

RNA-dependent DNA methylation

As discussed above, DNA methylation is thought to convey a form of epigenetic information. Though the DNMT enzymes are responsible for placing methyl groups on cytosine residues in DNA, how are these enzymes properly targeted to specific genomic sequences? For example, the sequences of “genetic parasites,” such as transposable elements, are specifically methylated (Law and Jacobsen, 2010), raising the question of how these sites are preferentially targeted for methylation. Work in plants has strongly implicated the role of RNAs in this targeting process (Law and Jacobsen, 2010). This RNA-dependent DNA methylation (RdDM) is thought to be triggered by transcription of the genomic locus with the resulting RNA being converted into double-stranded RNA (dsRNA) by the actions of RNA-dependent RNA polymerases. This dsRNA is then processed by components of the RNA interference (RNAi) machinery, which triggers the site-specific association of DNMT to regions of the genome that are homologous to the RNA (Law and Jacobsen, 2010). Indeed, de novo methylation can be triggered to regions of homology by the introduction of dsRNA (Mette et al., 2000). Interestingly, recent work has implicated a role for non-coding RNAs in establishing DNA methylation patterns at retrotransposable elements in mice (Aravin et al., 2008; Kuramochi-Miyagawa et al., 2008), suggesting that RdDM may also exist in mammals.

RNA inheritance and disease

Recent studies have indicated that maternally deposited RNA can be a source of epigenetic information. One such study demonstrated that the sterility induced by a phenomenon known as hybrid dysgenesis, in flies, could be accounted for by the lack of deposition of maternal non-coding RNAs (Brennecke et al., 2008). Hybrid dysgenesis refers to the sterile offspring produced from crosses between females from lab grown fly strains with males from strains found in the wild, whereas the reciprocal cross produces fertile progeny (Kidwell et al., 1977; Picard, 1976). This observation was explained by the fact that lab grown strains do not produce specific non-coding RNAs; therefore, lab grown females do not pass on these critical non-coding RNAs to their progeny, which leads to sterile offspring (Brennecke et al., 2008). In contrast, females from the wild possess these non-coding RNAs and transfer them to the next generation.

Furthermore, studies in mice have also suggested that paternal deposition of RNA can be a source of epigenetic information. Heterozygous animals that contain one copy of c-kit replaced with a lacZ:neo cassette have characteristic pigmented extremities (Rassoulzadegan et al., 2006). Interestingly, it was noted that crosses between heterozygous animals result in a greater proportion of offspring that show this phenotype than expected. Genotyping, however, indicated that an expected ratio of wild-type animals was present demonstrating that wild-type animals were displaying this mutant phenotype. Remarkably, crosses between these phenotypically mutant but genotypically wild-type animals resulted in progeny that had pigmented extremities, revealing transgenerational inheritance of this phenotype. Further studies revealed that transferring RNA from the sperm of heterozygous animals into one-cell embryos was sufficient to induce the pigmented phenotype (Rassoulzadegan et al., 2006). Consistent with these studies, more recent work has shown that the injection of microRNAs into one-cell embryos can result in transgenerational inheritance of different phenotypes (Grandjean et al., 2009; Wagner et al., 2008). These studies strongly implicate a role for RNA as a heritable source of epigenetic information.

Could the inheritance of RNA play an epigenetic role in human disease? One basic concept in genetics that is poorly understood, yet highly relevant to genetic diseases, is the idea of penetrance. For example, even patients with monogenic disorders, such as thalassemia, present with variable symptoms (Weatherall, 2000). How can a disease that is caused by a mutation in a single gene, result in variable phenotypes? While it has been proposed that other genetic modifiers may account for these differences (Weatherall, 2000), another possibility is that there is variation in the RNA that is inherited that leads to this phenotypic diversity. In support of this idea, injection of a microRNA in one-cell murine embryos is sufficient to induce transgenerational heritable cardiac hypertrophy (Wagner et al., 2008). Moreover, susceptibility loci identified by the recent explosion of genome-wide association studies account for only a small portion of the heritable component of these diseases (Manolio et al., 2009). It is therefore possible that these observations might be explained, at least in part, by variations in maternally or paternally inherited RNAs.

RNA editing and disease

By directly altering RNA nucleotides without affecting the original DNA sequence, RNA editing can significantly change protein-coding transcripts and especially non-coding RNAs (Farajollahi and Maas, 2010; Li et al., 2009). These RNA mutations can modulate the generation or destruction of splice sites, affect codon usage that lead to the production of novel proteins, alter RNA stability, and regulate target diversification and function of non-coding RNAs (Maas, 2010). Since inherited RNAs could be a source for epigenetic information (discussed above), it is plausible to postulate that RNA editing might contribute to the complexity of the epigenetic regulatory networks. Two enzyme families, Adenosine Deaminases Acting on RNA (ADARs) and APOlipoprotein B mRNA Editing enzyme Catalytic polypeptide (APOBEC), have the capacity to mutate adenosine residues in RNA to inosine (A-to-I) and cytosine residues to uracil (C-to-U), respectively (Farajollahi and Maas, 2010). Interestingly, knockout mouse models of ADAR1 and ADAR2 display severe phenotypes that result in embryonic lethality (ADAR1) or lethality shortly after birth (ADAR2) (Hartner et al., 2004; Higuchi et al., 2000; Wang et al., 2000).

In addition to inheritable RNA, the role of RNA editing in disease is becoming more appreciated. There have been several studies that have linked abnormalities in RNA editing to human diseases. One such study identified that several cancers showed hypoediting of Alu transcripts (Paz et al., 2007). Furthermore, analysis of human brain cancers revealed a similar hypoediting phenotype of the glutamate receptor (Cenci et al., 2008; Maas et al., 2001). All of these studies also implicated either a reduction in expression or activity in ADAR2, suggesting a role for ADAR2 in tumorigenesis. In addition, a recent study has implicated RNA editing in longevity in both humans and C. elegans (Sebastiani et al., 2009). Given that many transcripts that are edited are brain specific genes, it is not surprising that some neurological disorders, including schizophrenia (Sodhi et al., 2001) and depression (Gurevich et al., 2002), have been associated with RNA editing defects (Farajollahi and Maas, 2010). The role of RNA editing in disease is gaining momentum, especially with the advent of high-throughput sequencing technologies. The molecular mechanisms underlying the role of edited transcripts in the pathogenesis of these diseases are currently not well understood. However, these studies highlight the importance of looking at RNA editing as a potential mechanism of diversifying the epigenetic landscape.

Proteins: The Third Epigenetic Dimension

The protein code

According to the central dogma (inner circle in Figure 1), alterations initiated within the DNA sequence that culminate in a modified proteome could result in a phenotypic effect on an organism (Altshuler et al., 2008). Yet, we now know that proteomes can be effectively modified and store epigenetic information without any underlying change to the DNA sequence, leading sometimes to disease emergence (Ptak and Petronis, 2008) (Figure 1).

Histone modifications and disease

The tight intertwining of DNA and histones — to form chromatin — evolved to promote the compaction of DNA within the nucleus of a cell. But it also serves as a plastic and reversible mode for complex gene regulation. Covalent posttranslational histone modifications control chromatin architecture and many aspects of organismal development from simple gene expression to cell fate determination, differentiation, and, in some cases, disease onset (Pedersen and Helin, 2010). Since the list of possible histone modifications is extensive (Bartke et al., 2010; Strahl and Allis, 2000) and since short stretches of DNA are wrapped around a histone octamer (dimers of H2A, H2B, H3, and H4), the combination of modifications could potentially be complex. This prompted the proposal of an epigenetic “histone code” (Jenuwein and Allis, 2001; Lee et al., 2010; Strahl and Allis, 2000) that could be “memorized” during cell proliferation and differentiation (Bird, 2007; Ng et al., 2003). Among all the histone modifications, methylation (mono-, di-, or tri-) and acetylation have the most studied effects on gene regulation. Not only do these modifications often compete for the same histone lysine residues, they could also recruit antagonistic regulatory complexes (Strahl and Allis, 2000). They can also be transmissible across generations in a yet obscure manner (Cavalli and Paro, 1998). Moreover, histone mark writers (e.g., methyltrasferases or acetyltrasnferases) are often counteracted by a plethora of histone mark erasers (e.g., demethylases or deacetylases). Alterations in histone marks through environmental factors (Jirtle and Skinner, 2007) or through aberrations in histone mark writers or erasers could lead to debilitating diseases. For example, histone methylation was shown to be important for the maintenance of DNA methylation (Ooi et al., 2007; Xin et al., 2003). This is particularly important at imprinted loci, which could lead to disorders such as the Prader-Willi syndrome (Xin et al., 2003). In addition, deregulation of histone modifications has been associated with mental retardation (e.g., Coffin-Lowry, Rubinstein-Taybi, and alpha thalassemia/mental retardation X-linked syndromes), neurological disorders such as Huntington’s, Parkinson’s, and Alzheimer’s diseases, as well as multiple sclerosis and epilepsy (Iwase and Shi, 2011; Schaefer et al., 2011; Urdinguio et al., 2009). Aberrations in the histone code have also been associated with tumorigenesis (Chi et al., 2010; Kurdistani, 2011), including Walbenstrom’s Macroglobulinemia (Sacco et al., 2010).

Digressing from histone modifications, recent studies have observed histone modification mimicry in non-histone proteins (Sampath et al., 2007). Moreover, the tubulin tails of microtubules, composed of α- and β-tubulin, can also be modified by various posttranslational modifications, which subsequently allow the recruitment of microtubule-associated proteins (MAPs) thereby affecting cell function. Such patterns of microtubule modifications prompted a comparison to the “histone code” hypothesis (Strahl and Allis, 2000). However, it is contentious whether the information encoded by non-histone modifications could be considered epigenetic.

Chromatin remodeling, the Polycomb/Trithorax systems, and disease

It is not fully known yet how histone modification patterns are established and maintained in different tissues of the body despite the conservation of genetic information. But the Polycomb/Trithorax systems, which are considered by some to be a classical form of transmissible protein epigenetics (Bird, 2007), provide an insight into the mechanism. The Polycomb (PcG) and Trithorax (TrxG) group of proteins are essentially in competition over the expression state of homeotic genes, which are responsible for the normal development of multicellular organisms. They maintain the “memorized” repressed or activated state of effector genes, respectively. PcG and the TrxG complexes are composed of various histone “writers” and “erasers” but they also contain chromatin remodeling proteins, such as the SWI/SNF, ISWI, and NURF complexes (Bird, 2007; Ko et al., 2008; Kokavec et al., 2008). Typically, chromatin remodeling proteins have domains that can “read” the histone modification pattern and re-organize the chromatin architecture in a non-covalent manner by altering nucleosomal positioning, ultimately resulting in epigenetic effects (Ko et al., 2008; Kokavec et al., 2008; Segal and Widom, 2009). In addition to histone modifications, defects in chromatin remodeling have been implicated in many illnesses including Charge Syndrome (Martin, 2010), mental retardation (Schaefer et al., 2011), and cancer (Ko et al., 2008; Kurdistani, 2011).

Prion-like factors and disease

A disparate form of protein epigenetics that has been receiving increased interest recently is self-replicating conformational changes of prion-forming proteins. This scenario is so non-canonical that it took the scientific community decades to fully appreciate its potential (Benetti and Legname, 2009; Prusiner, 1998; Tuite and Serio, 2010). Prions, unlike other proteins, function outside the boundaries delineated by the central dogma of molecular biology (Halfmann and Lindquist, 2010). Prionogenic proteins have the unusual ability to adapt very different stable conformational states (Halfmann et al., 2010) via the process of protein-based molecular memory. In the native state, prionogenic proteins have modular domains that are highly disordered and flexible in conformation. The transformation from the native to the prion state occurs via nucleation; whereby a single transformed prion self-replicates its conformation onto the native state proteins by binding to it. Such process does not seem to require genetic, expression level, or posttranslational modifications to the prionogenic protein (Halfmann et al., 2010). Therefore, prions are emerging as an “extreme case of epigenetic inheritance” (Deleault et al., 2007; Halfmann and Lindquist, 2010), which could act as cytoplasmically inherited epigenetic capacitors of cells growing under stress (Tuite and Serio, 2010), as well as for the maintenance of neuronal structural change and the persistence of long-term memory (Bailey et al., 2004; Si et al., 2010). These prion-based mechanisms may even influence genetic information and evolutionary adaptability (Halfmann and Lindquist, 2010). In pathologic cases, prion formation culminates in an uncontrolled chain reaction where a nucleus of prion fibrils, known as amyloid, is formed (Halfmann et al., 2010; Halfmann and Lindquist, 2010). In mammals, the major prion protein (PrP) is encoded by the PRNP gene and accounts for the majority of prion diseases collectively known as transmissible spongiform encephalopathy (TSE) (Collinge, 2001; Prusiner, 1998). In humans these include classic Creutzfeldt-Jakob disease (cCJD), a recent and more pathogenic variant Creutzfeldt-Jakob disease (vCJD; related to mad cow disease), Gerstmann-Sträussler-Scheinker syndrome (GSS), fatal insomnia (FI), and kuru (Collinge, 2001; Goedert et al., 2010; Montagna et al., 2003). Currently, these diseases are incurable, leading to irreversible neuronal loss and invariably death (Collinge, 2001). In rare cases, prion diseases can be genetically heritable (Montagna et al., 2003). However, the vast majority of TSE is caused by sporadic or acquired prions which propagate by self-replicating their tertiary conformation. Paralleling TSE, more common neurodegenerative diseases, including Alzheimer’s and Parkinson’s, could also be characterized by the misfolding and aggregation of filamentous proteins such as Tau and α-synuclein, respectively (Goedert et al., 2010); leading to the suggestion that more prevalent neurodegenerative diseases might also be mediated by an epigenetic prion-like process (Aguzzi and Rajendran, 2009; Goedert et al., 2010).

Discovering the Future of Genetics and Epigenetics in Medicine

The complex interaction between the genome, epigenome, and the environment encompasses the beauty of life forms. Abnormalities in these relationships can lead to pathological conditions. The development of new high-throughput technologies, together with collaborative research initiatives such as ENCyclopedia Of DNA Elements (ENCODE, http://www.genome.gov/10005107), Disease Annotated Chromatin Epigenetic Resource (DAnCER, http://wodaklab.org/dancer), High-throughput Epigenetic Regulatory Organization in Chromatin (HEROIC, http://www.heroic-ip.eu), the Human Epigenome Project (HEP, http://www.epigenome.org), or the NIH Common Fund’s Epigenomics Program (http://commonfund.nih.gov/epigenomics), hold great promise to improve our understanding of the genetics and epigenetics underlying health and disease. Although DNA methylation in mammals has been studied for several decades, there is still much to understand about the storage of epigenetic information in DNA. In this sense, the rapid advance in microarrays and massively-parallel sequencing technologies are facilitating genome-wide DNA methylation profiling of selected cell types, diseases, and species (Suzuki et al., 2010; Zilberman and Henikoff, 2007). Similarly, next-generation sequencing technology is becoming invaluable in the study of RNA and its role in the physiology of the cell (Hawkins et al., 2010). Beyond the role of coding RNAs, the study of non-coding and regulatory RNAs is becoming a new promising area of epigenetic research. Finally, the increasing spectrum of antibodies against posttranslationally modified proteins as well as the application of high-resolution profiling of histone variants and nucleosome positioning will allow us to better understand the chromatin epigenetic landscape (Hawkins et al., 2010; Park, 2009). For molecular medicine, the fast development of these new approaches and the reversible nature of the epigenome offer the promise of great advances in the fields of biomarker discovery, drug targeting, and personalized medicine.

Conclusion

While much progress has been made in understanding the genetic basis of diseases, much work remains. With the advent of genome-wide association studies, many thought that the genetic underpinnings of “complex diseases” would be discovered and the era of personalized medicine would be fully realized. However, these studies have not been as fruitful as some had hoped. Is the lack of success of such studies due to technological limitations or is there a greater underlying problem? By focusing on merely the genetic component of diseases, we are neglecting the ever more complex nature of epigenetic information. The views presented in this article support the opinion that a better understanding of the multidimensional nature of epigenetic information in the form of any of the macromolecules of the cell will lead to fundamental discoveries on the etiology of various diseases.

Acknowledgments

We are grateful to Professors Matthew D. Scharff and Arthur I. Skoultchi for their support and encouragement. We also thank the Albert Einstein community, particularly Dr. Michael Papetti and the Relativity Club, for stimulating discussions. This work was supported by National Institutes of Health Grants R01 CA079057, R01 CA72649, and R01 CA102705.

Disclosure

The authors report no conflicts of interest.

Corresponding Authors

Richard Chahwan, Ph.D.; Sandeep N. Wontakal, Ph.D.; and Sergio Roa, Ph.D., Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., New York, New York 10461, USA.

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[Discovery Medicine; ISSN: 1539-6509; Discov Med 11(58):233-243, March 2011.]

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