Our advances in technology allow us to sequence DNA to uncover genetic differences not only between individuals, but also between normal and diseased cells within an individual. However, there is still a lot we have yet to understand regarding the epigenetic mechanisms that also contribute to our individuality and to disease. The 80th Biochemical Society Annual Symposium entitled Epigenetic Mechanisms in Development and Disease brought together some leading researchers in the field who discussed their latest insights into epigenetic mechanisms. Methylation of DNA has been the focus of much study from both a developmental perspective and imprinting of genes to its contribution to diseases such as cancer. Recently, the modification of methylcytosine to hydoxymethylcytosine within cells was uncovered, which opened a host of potential new mechanisms, and a flurry of new studies are underway to uncover its significance. Epigenetics is not confined to a study of DNA, and the post-translational modifications on the histone proteins have a significant role to play in regulating gene expression. There are many different modifications and, as shown at the Symposium, new variations used by cells are still being uncovered. We are some way to identifying how these modifications are added and removed and the protein complexes responsible for these changes. A focus on the function of the complexes and the interactions between individual modifications to regulate gene expression is advancing our knowledge, as discussed in the accompanying papers, although there are clearly plenty of opportunities for new breakthroughs to be made.

Epigenetics is the study of changes in gene expression which occur in the absence of mutation, but are mitotically inheritable. Epigenetics was first put forward as an idea in the 1940s by C.H. Waddington as a mechanism to maintain cells in their specialized phenotype through cell division. DNA methylation, in which methyl groups are added to the cytosine residues mostly present within the dinucleotide sequence CpG, was first described in 1975 [1,2] and it was suggested that cytosine methylation of DNA might be a mechanism of gene control. In 1979, it was suggested that DNA methylation changes may contribute to carcinogenesis [3] and many reports have since provided evidence that tumour-suppressor gene promoters are methylated and inactivated in cancers. More recently, it has become evident that, in addition to the focal hypermethylation, there is also a more widespread DNA hypomethylation associated with the formation of a repressive chromatin structure in cancer cells [4].

Initially, a DNA methyl mark was considered permanent in that it was not thought to be removed and could only be ‘erased’ by preventing its reapplication after a round of DNA replication. Such a scenario exists during development as demethylation occurs first in the primordial germ cells and then later in fertilized zygotes. This is followed by establishment of new methylation patterns on genes, a crucial time in an organism's existence. Environmental factors to which a developing embryo is exposed can influence the deposition of methyl marks, a situation most elegantly described for the epigenetic regulation of the agouti gene in mice whose expression levels can be altered as a result of changing the level of methyl donors in the maternal diet [5]. Now studies in animal models are uncovering the extent to which epigenetics are inherited and how this inheritance is manifested down the parental line [6,7]. Altered nutrition in the early life of developing humans has long been associated with increased risk of diseases, shown most clearly from the Dutch Hunger Winter, such as diabetes and cardiovascular disease, and the signal is believed to be the altered epigenetic marks laid down in utero [8]. Studies on cultured stem cells have highlighted the plasticity of the developing epigenetic landscape and the influence of the environment upon it. Small changes in the in vitro culture conditions for these cells have global effects on a number of epigenetic marks [9]. The long-term consequences of these alterations are not known, but such observations identify a need to address the potential implications for assisted reproductive technologies which require an in vitro culture step. Other epigenetic marks also contribute, in ways we do not fully understand, to influence the outcome of epigenetic reprogramming of an individual genome [10]. Some genes show parental imprinting in which one of the parental copies (for some genes it is the male and for others it is the female copy) is silenced by methylation. Such imprinting is considered to result from the genetic conflict between male and female genes for access to maternal resources and include genes that regulate the development of placental endocrine lineages [11]. Imprinted genes influence and regulate the growth of the cell, and loss of imprinting which disrupts such regulation has been found to be a major cause of cancer. For example, loss of imprinting and an increased expression of the growth-promoting gene IGF2 (insulin-like growth factor 2) is associated with Wilms's tumour, breast and colorectal cancers [12]. As well as growth, brain development and adult behaviour have also been associated with the activity of imprinted genes and imprinting disorders such as Prader–Willi syndrome have led to suggestions that susceptibility to neuropsychiatric disorders arise because of gene dosage effects resulting from inappropriate imprinting [13].

Most of our genes are not imprinted and our epigenetic marks are not static. Studies in monozygotic twins have very neatly shown that epigenetic profiles of the genome change over time. On the basis of their DNA methylation pattern at 3 years of age, twins are epigenetically indistinguishable, but, by 50 years, they show very striking differences [14]. Changes in epigenetic marks are not only a driver of disease, but also a normal consequence of healthy aging, and understanding how specific modifications contribute to our phenotype is of major importance [15].

That methyl groups could not just be added to cytosine residues, but also actively removed has been a hotly debated topic for many years. Although there has been substantial evidence in support of such a notion, the lack of an identified demethylating enzyme and the biochemical mechanism was always the final stumbling block. The recent discovery that 5mC (5-methylcytosine) could be converted into 5hmC (5-hydroxymethylcytosine) by human TET (ten-eleven translocation) 1 suggested a new mechanism for the regulation of DNA methylation. Conversion of 5mC into 5hmC has the potential to recruit specific 5hmC-binding proteins, disrupt interactions of 5mC or act as an intermediate in a DNA demethylation pathway [16]. Whether 5hmC is a transient intermediate or stable epigenetic mark is still a hotly debated issue and we do not understand the precise role of 5hmC or the function of TET proteins in regulating the epigenetic landscape during development or their potential contribution to disease states. Given the significant role that DNA methylation has been shown to play in cancer, it seems likely that 5hmC will also contribute, and a number of researchers have begun addressing this question. Indeed, mutations in two of the three TET proteins (TET1 and TET2) have been associated with cancers, although whether these mutations contribute to the cancers or are just a correlative happenstance is not yet clear [1719].

DNA methylation does not act as a sole epigenetic mark, but acts in conjunction with a range of post-translational modifications that occur on the histone proteins. Known modifications include acetylation, methylation, phosphorylation, ubiquitination, SUMOylation and ADP-ribosylation [20], but are being added to as ongoing research probes deeper and deeper into chromatin, and there may still be more to uncover. Complexity is increased further when the location of modifications are considered. Most modifications are confined by the amino acid, for example acetylation occurs exclusively on lysine residues, and methylation has been found to occur on lysine residues, arginine residues and now glutamine residues [21]. Furthermore, lysine residues can be mono-, di- or tri-methylated, whereas arginine residues can be mono-, symmetrically di- or asymmetrically di-methylated [20,22]. Perhaps the most unusual modification does not alter the chemical composition of chromatin at all, but results in an isomerization of a proline residue in histone H3 [23], converting the peptide bond preceding the proline residue between the cis and trans conformation and altering the structure of the histone [24]. A lot of early work on individual modifications has focused on identifying a functional role for each specific modification although it has become clear that there is a lot of interplay and cross-talk between different histone modifications [22,25] as well as between histone modifications and DNA methylation [26], suggesting that we probably need a more systems-wide view of these modifications if we hope to uncover the histone code.

The epigenetic marks themselves are only one half of the story: each mark has the potential to be deposited (written), removed (erased) or recognized (read) by specific protein domains present in a host of different proteins. Understanding how this is achieved and regulated within the cell is currently a major focus of many top research groups. Many of the proteins that can modify chromatin are themselves part of larger protein complexes, for example the ubiquitous HDAC (histone deacetylase) 1 and 2 are found within the Sin3, NuRD (nucleosome remodelling and deacetylation) and CoREST (co-repressor for element-1-silencing transcription factor) complexes [27]. More focused studies on specific complexes are beginning to allow us to uncover some of the mechanisms that contribute to a dysregulated epigenetic landscape in specific disease states such as the changes in acetylation and lysine methylation associated with cardiac hypertrophy [28,29], enhanced HDAC activity associated with rheumatoid arthritis [30] or how they interact with other important cellular events such as DNA damage [31]. The sheer multiplicity of these complexes and their potential interactions with chromatin will keep us busy for a while yet.

What does the future hold? With the rise of next-generation sequencing, we are clearly going to have substantial amounts of DNA sequence data generated in the near future which will supplement the methyl microarrays and genome-wide chromatin immunoprecipitation studies published to date. The challenge will be to interrogate these data in sensible ways and to present such large quantities of data in a way that it can be understood and read by individuals without the need for expertise in computer programming and informatics. The contribution of non-coding RNA to chromatin structure and its potential role in regulating epigenetic marks is another topic on the radar [32]. Short microRNAs have well-described functions regulating mRNAs though the function of long non-coding RNAs is a little less clear. Many of them have been associated with chromatin-modifying complexes [33], suggesting that they could influence epigenetic marks and regulate gene expression.

Biochemical Society Annual Symposium No. 80: Biochemical Society Annual Symposium No. 80 held at University of Leeds, U.K., 11–13 December 2012. Organized and Edited by Paul Hurd (Queen Mary, University of London, U.K.), Adele Murrell (Cancer Research UK) and Ian Wood (Leeds, U.K.).

Abbreviations

     
  • HDAC

    histone deacetylase

  •  
  • 5hmC

    5-hydroxymethylcytosine

  •  
  • 5mC

    5-methylcytosine

  •  
  • TET

    ten-eleven translocation

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