Why do some foods promote health problems and others make us healthy? How does stress impact our long-term well-being? Why is it that the older we get, the more likely it is that age-related illness will strike us? Unlocking the secrets behind these and other questions has the potential to revolutionize life as we know it. The emerging field of epigenetics is aiming to do just that.

The importance of nature versus nurture has long been disputed. It cannot be denied that environment greatly influences how a child grows and develops, nor can it be denied that our DNA is the blueprint that makes us who we are. Epigenetics merges these two seemingly contradictory lines of thought to explain how environmental factors cause physical modifications to DNA and its associated structures, which result in altered functions.

Certain traits, like height and hair color can largely be explained through simple genetics: If two parents are tall with blond hair, chances are their children will be too. However, not all genes are created equal and most traits are not controlled by a single gene. Instead, most traits, such as metabolism, personality, intelligence, and even many diseases, are much more complex and rely on the interactions of hundreds of different genes. The complexity doesn’t stop there either! If it did, then identical twins would be exactly the same; but they are not! Although they tend to be extremely similar, identical twins can still differ greatly in health and personality. This is because, although they carry an identical set of genes, these genes may be expressed at different levels. Genes are not simply turned “on” or “off” like a light switch, but instead function more like a dimmer switch with a dynamic range of expression. The amount that a gene is expressed can differ from one person (or twin) to another and can even fluctuate within a single individual. The mechanisms by which these kinds of changes take place are extremely complicated and are influenced by a variety of factors including one’s internal and external environment. Epigenetics is the study of these kinds of changes and the mechanisms behind them. Nearly every aspect of biology is influenced by epigenetics – making it one of the most important fields in science.

 

Understanding epigenetics requires an understanding of chromatin structure. Chromatin, which is organized into repeating units called nucleosomes, is the complex of DNA, proteins, and RNAs that comprises chromosomes1. A nucleosome consists of 147 bp of double-stranded DNA wrapped around an octamer of histone proteins, usually two copies each of the core histones H2A, H2B, H3, and H4. Histones and DNA can be chemically modified with epigenetic marks that influence chromatin structure by altering the electrostatic nature of the chromatin and/or by altering the affinity of interactions with chromatin-binding proteins. In mammalian cells, most of the chromatin exists in a condensed, transcriptionally silent state called heterochromatin. Heterochromatin generally has high levels of DNA methylation and the nucleosomes in heterochromatin contain histones with post-translational modifications that are conducive for gene silencing. Euchromatin is less condensed, and contains most actively transcribed genes. Euchromatin exhibits lower levels of DNA methylation, relative to heterochromatin, and the nucleosomes in euchromatin contain histones with modifications that promote gene expression.

DNA methylation2

 

DNA can be modified by methylation of cytosine bases5. The enzymes that methylate DNA are called DNA methyltransferases. In humans, the DNA methyltransferases DNMT3A and DNMT3B methylate the genome during embryonic development, whereas the maintenance DNA methyltransferase, DNMT1, methylates hemimethylated DNA (methylated on only one strand) following mitosis. Methylated DNA generally represses gene expression, as it attracts methylcytosine binding proteins that promote chromatin condensation into transcriptionally repressive conformations. In mammals, only cytosines preceding guanines (CpG dinucleotides) are known to be highly methylated. CpG dinucleotides are underrepresented relative to other dinucleotide combinations and are widely dispersed throughout the human genome. The majority of CpGs are located in non-coding regions and are typically methylated. However, many of the remaining CpG dinucleotides are found in clusters upstream of a gene’s coding sequence, in domains referred to as CpG islands. These CpG islands are typically unmethylated, or hypomethylated, to allow for the expression of downstream genes. DNA regions near CpG islands, referred to as island “shores” are often methylated and may serve to fine-tune the expression levels of nearby genes.


Histones are also subject to several different covalent modifications, including methylation, acetylation, phosphorylation, ubiquitination, and sumoylation1, 4. The hypothesis of the “histone code” was developed to suggest that combinations of histone modifications ultimately control gene expression. While it is not clear that this hypothesis is universal, several supporting examples have been reported. Histone modifications can have varying effects based on the type of modification and the location of the modification on the histone. The best-characterized histone modifications are acetylation and methylation. Acetylation of histone lysine residues is associated with euchromatin because it weakens the charge attraction between histone and DNA, serving to decondense chromatin and facilitate transcription. Acetylated histone residues can also serve as binding sites for other histone-modifying enzymes or chromatin-remodeling factors that promote gene expression. Histone methylation can be either repressive or activating, depending on the location of the methylated residue. For example, methylation of the lysine at the fourth residue of histone H3 (H3K4Me) promotes a transcriptionally active conformation, whereas H3K9Me promotes a transcriptionally repressive conformation. H3K36Me can be activating or repressive, depending upon proximity to a gene promoter region.

Histones are not the only proteins that interact with DNA in chromatin. Nucleosome-remodeling complexes manipulate chromatin structure, thereby affecting gene silencing and expression. Chromatin remodeling proteins affect chromatin structure in various ways. They can expose DNA wrapped in nucleosomes by sliding histones along the DNA, or detach the histone octamer completely from a DNA sequence. They can also remove specific subunits of the histone octamer, replacing them with histone variants, resulting in a non-canonical structure. Not all nucleosome-remodeling proteins possess the same functions. The SWI/SNF family can slide nucleosomes, eject histones, and displace H2A-H2B dimers. The ISWI family is capable of sliding, but not histone ejection. Some ISWI family proteins can displace H2A-H2B dimers, while others cannot. The Mi-2/NuRD complex has DNA sliding activity, and, unique among chromatin remodeling complexes, also carries histone deacetylase activity2.

 

RNAs, especially non-coding RNAs, are known to play several interesting roles in the control of chromatin structure. In plants, a process called RNA-directed DNA methylation uses siRNAs generated by RNA Polymerase IV and the DICER LIKE 3 protein to localize the DNA methyltransferase DRM2 to its specific target sequence3. Another epigenetic trait dependent upon RNA is X chromosome inactivation1. This process occurs in female mammals to control expression dosage of the genes encoded on the X chromosome between males (who only possess one X chromosome) and females. In females, one of the two X chromosomes is inactivated in a process featuring the expression of the large non-coding RNA Xist, which binds to the entire length of the chromosome from which it is transcribed. Xist recruits chromatin-remodeling proteins and blocks transcription machinery from binding to the inactivated chromosome.

 

References
1. Allis, CD et al. In CD Allis, T Jenuwein, & D Reinberg (Eds.), Epigenetics (p. 23-62). New York: Cold Spring Harbor Laboratory Press (2007).
2. Cairns, BR. Nat Struct Mol Biol 14: 989-996 (2007).
3. Henderson, IR & Jacobsen, SE. Nature 447: 418-424 (2007).
4. Kouzarides, T & Berger, SL. In CD Allis, T Jenuwein, & D Reinberg (Eds.), Epigenetics (p. 191-210). New York: Cold Spring Harbor Press (2007).
5. Miranda, TB & Jones, PA. J Cell Physiol 213: 384-390 (2007).