Epigenetic modifiication & Histone methylation

The term ‘Epigenetics’ was not known in science until early 1940’s when British biologist Conrad Hal Waddington described his first developmental biology theories as an ‘epigenetic landscape’ (Waddington 1940). His hypothesis of genes controlled by epigenetics during embryo development started to evolve even before the discovery of DNA (Watson Crick 1953) and much before DNA methylation discovery (Miller et al 1978). Later on, the first definitions of the term ‘epigenetics’ tried to describe it as specific methylation of DNA which can lead to gene silencing in the developing organism as well as in fully developed organisms. However, the word epigenetic was not commonly used in scientific papers until early the 1990’s (according to Google Books Ngram Viewer).

In parallel to the discovery of DNA, other important studies on chromatin were performed. It was shown that the cell nucleus possesses proteins called histones (Kossel, 1884). However, their function was not known until 1950 when it was suggested that histones repress genes (Stedman & Stedman, 1950) and that DNA is bounded around histones (Himes 1967). Later on, histone modifications such as N-terminal acetylation and methylation were discovered and it was proposed that these modifications may affect RNA synthesis (Allfrey et al. 1964). Finally, in the early 1990s, it was believed that histones and their N-terminal amino acid tails modifications play an important role in gene regulation and since then interest in researching the field of epigenetics has increased substantially.

All mentioned discoveries led to the current definition of epigenetics whereby modifications to DNA and histone tails can influence gene expression without altering the DNA sequence.

Nowadays, in addition to histone methylation and acetylation, many other histones modifications to lysine, arginine, serine and threonine residues are known e.g.: phosphorylation, acetylation, ubiquitination, sumoylation, glycosylation and diverse acylation, which all may result in gene silencing or expression (Janssen et al. 2017).

However, among all epigenetic modifications methylation is the only modification known to target both, histone residues and DNA, identifying methylation as one of the most interesting epigenetic changes.

DNA methylation occurs mainly at C5-cytosine (5-mC) and N6-adenosine (6-mA) and is catalysed by specific DNA methyltransferases (DNMT), which is generally linked to a gene repression. However, investigations of the most explored C5-cytosine modification uncovered that C5-cytosine can undergo demethylation through intermediates: 5-hydroxymethylcytosine (5-hmC) (Kriaucionis & Heintz 2009; Tahiliani et al. 2009), 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC). Each of mentioned above steps of C5-cytosine demethylation is carried out by a group of ten-eleven translocation (TET) enzymes (Ito et al. 2011). Subsequently, thymine DNA glycosylase (TDG) converts 5-carboxycytosine to unmodified cytosine (Kohli & Zhang 2013). Discovery of these new cytosine derivatives gave completely new insight to the understanding of epigenetic modifications as before DNA methylation was considered as an irreversible process.

Histone methylation can be found on lysine and arginine residues. Moreover, methylation of lysine residues consists of three forms: mono-, di- and trimethylated lysine. In turn, arginine possesses two forms: mono and di –methylated, however, dimethylated form occurs in symmetric and asymmetric dimethylarginine isoforms (Di Lorenzo & Bedford 2011). Each of the mentioned histone methylation forms is a product of a reaction catalysed by a specific enzyme. In the literature, initially, these were called histone methyltransferases (HMTs). However, due to the current knowledge that these enzymes target not only histones but also other proteins in the cell cytoplasm, researchers tend to use new terminology and abbreviations: KMT for lysine methyltransferases and PRMT for (protein) arginine methyltransferases (Allis et al. 2007).

Interestingly, an answer to the big question – whether histone/protein methylation can be a reversible process in vivo remained unknown until 2004, when researchers identified specific lysine demethylase (LSD1) (Shi et al. 2004) bringing a huge impact to current knowledge about epigenetic modifications. Later on, new families of lysine demethylases were discovered and called KDMs. However, no evidence for arginine demethylation in vivo has been found yet.

Epigenetic enzymes are currently undergoing closer investigations into their mechanisms of action and structure. Researchers are discovering more and more links between epigenetics and metabolism (creating a new area of research called: metaboloepigenetics) and disease development such as cancer (Donohoe & Bultman 2012; Wang et al. 2013). At present, one of the epigenetic challenges scientists are facing is designing specific inhibitors for epigenetic enzymes (Chen et al. 2004; McAllister et al. 2016).

Moreover, research suggests that epigenetic modifications may interplay with the non-coding RNA which may have an impact on the development of various diseases (Maia et al. 2014; Mathiyalagan et al. 2014). Investigations into the link between non-coding RNA and epigenetics could bring us a new insight into non-coding RNA functions in our genome.

Altogether, researchers hypothesize that the of genetic code of eukaryotic cells possess an epigenetic code (Turner 2007). This epigenetic code encompasses all histone and DNA modifications which can regulate DNA expression and influence cell functionality.

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