Biology Basics: What’s the deal with Epigenetics?

ORIGINAL: OBR Review
Written by Brian Abraham

January 17, 2013

Photo credit: © WGBH Educational Foundation

Why do we care?
With few exceptions, namely functionally variable regions in the immune system and in disease, all of a person’s cells have the same DNA sequences and genes. Yet the variety of cells in terms of shape and function is vast. How is it that a muscle cell and a blood cell have the same genes yet do such strikingly different things?

In short, not every gene is being used or transcribed by all cell types: There are certain genes that are essential for blood cells that muscle cells don’t express (transcribe) or use. For example, genes making proteins that recognize foreign bodies would be useful for an immune blood cell but would be a waste of a muscle cell’s energy. The burgeoning fields of epigenetics and epigenomics investigate these patterns of on/off genes and what regulates their expression. Epigenomics refers to the genome-wide application of epigenetics, which generally refers more to single-gene analyses.

Where does it apply?

“Epigenetic” as an adjective refers to heritable traits that are not changes to the DNA sequence itself. Heritability can be across both cell divisions as well as trans-generational. When a fat cell replicates and both daughter cells retain fat cell traits, inheritance is referred to as divisional/replication inheritance. When offspring retain traits of their parents, the inheritance is termed trans-generational inheritance.

A famous example of such trans-generational epigenetic inheritance is the Dutch Hongerwinter. In 1944, the Dutch in areas of the Nazi-occupied Netherlands were starving as the result of a blockade. Fetuses that developed in the wombs of mothers surviving the famine showed a number of characteristic traits of nutrient deprivation themselves, including glucose sensitivity. Later biochemical analyses demonstrated epigenetic marks on genes regulating insulin-like growth factors– characteristics of nutrient deprivation– despite no change in the DNA of these genes. Further tests of second-generation offspring may show that these marks and traits acquired in response to starvation are inherited across multiple generations.

Before Darwin’s famous description of evolution by natural selection, Jean-Baptiste Lamarck proposed the idea that traits acquired by the parent can be passed down to offspring. For instance, a giraffe’s neck is long because its parents had to stretch to reach higher trees. When On the Origin of Species elegantly explained population shifts by survival, the idea of heritability of acquired traits lost popularity. The theory was further buried when Mendelian genetics demonstrated the mechanism of genetic inheritance. It has lain dormant until a recent resurgence in interest implicating epigenetics as a plausible explanation for trans-generational inheritance of acquired traits.

How does it work?

Roughly 3 meters of DNA sequence is stored inside every nucleated human cell; the condensation and packaging of the DNA sequence is essential to regulation of gene expression. In general, uncondensed genes are expressed more readily than condensed genes. Following is a discussion of the various methods by and degrees to which genes are condensed into “chromatin”– the name given to the DNA/condensing protein complex.

Cytosine methylation

Chemical modifications can be made to DNA bases themselves. While several are known and more are being discovered, the most exhaustively investigated one is methylation, especially of cytosines. This cytosine methylation often occurs at the carbon-5 position, and prevents binding of the transcription apparatus, meaning that the DNA is not transcribed or expressed. 5mC is one of the strongest indicators of a gene’s silent status and is very stable, including across cell divisions.

The mechanism of inheritance of 5mC is relatively well understood. After DNA replication, where a copy of DNA is made using one strand as a template, the cytosines on the new strand are not methylated. DNMT1 is responsible for resolving the full methylation status of cytosines. In contrast, DNMT3 is responsible for establishing new 5mC at genes being silenced. Activity of DNMT3 has been shown to respond directly to external stimuli and alter its activity during development. DNMT3 activity has been implicated in memory formation and its expression has been shown to respond to chronic cocaine use.

Studying modified DNA bases in a genome-wide fashion is somewhat difficult. Current sequencing technologies, which rely on the complementarity of C to G and A to T, cannot detect the methylation status of cytosines directly. Some workarounds include the treatment of genomes with bisulfite, which converts cytosine (C) to uracil (U) while 5mC is unmodified. Uracil is complementary to A, which will read as thymidine using complementary-reliant sequencing. Other techniques involve methylation-binding proteins as a proxy.

Recent developments in sequencing technologies that do not rely on complementarity have made it easier to detect chemical modifications to bases. In particular, Single Molecule Real Time (SMRT) sequencing involves a specifically designed polymerase that can detect all nucleotides on a given DNA strand. In the 2012 Nature report, Fang et al. demonstrate that this technique can be modified to incorporate methylation information.

Nucleosomes and histones

Silencing is also conferred by the positions and composition of the proteins involved in condensing DNA. 146 base pairs of DNA are wound around an octomer of histone proteins, which is then termed a nucleosome. The N-terminal tails of histone proteins poke outside of the core of the nucleosome and can also be modified with several moieties, including methyl, acetyl, and ubiquitin groups. Residues on the tails and the modifications made strongly correlate with either activation or repression of the genes to which they are bound. As nucleosomes need to be removed for transcription to progress, the stability of the nucleosome with particular modifications made to its tails may allow for a more or less accessible DNA gene. Whether these marks are causes or results of transcription or silencing remains to be confirmed.

The heritability of nucleosome positions, composition, and array of modifications is also under debate. However, recent work has shed light on some aspects. Computational analysis has demonstrated that nucleosomes occupy certain dyad segments and their position can be predicted by these dyad frequencies and free binding energy. Another recent paper has indicated that the modifications of histones are not themselves inherited during DNA replication, but the binding profiles of proteins responsible for modifying histones are.

Epigenetics in the news

To date, many traits and diseases with heritable patterns are known, but the genes associated with them are not. Perhaps it is not the DNA sequences themselves that are to blame, but some dysregulation of epigenetic processes. As an example, researchers have found a striking correlation between 5mC on a particular gene (PDYN) and alcohol dependence in a 28-patient cohort. More recent work has started to link more complex traits such as homosexuality with epigenetics. Twin studies have demonstrated only about 50% concordance of homosexuality between male twins, indicating other means for the trait. And, a recent study has begun to link homosexuality with so-called “epi-marks”.

As technology for genome-wide interrogation of both chemical modifications to nucleotides and the binding and composition of nucleosomes improves, we will gain the data to explain more traits, and likely more complex ones. Many of the currently understood diseases are caused by mutations to one gene in a binary manner. Epigenetics provides a tool and ideological framework for understanding more widely ranging diseases and traits and will continue to explain the variety of humanity.