Epigenetic mechanisms using DNA methylation, histone modifications, and RNA regulation.

The field of epigenetics has become an essential area of focus for scientists working on cancer, neurodegenerative disease, and addiction research. Epigenetic mechanisms involve temporarily activating or repressing gene expression. Interestingly, these changes can be passed from generation to generation, even though they do not permanently change the DNA sequence. The three main mechanisms of epigenetics are DNA methylation, histone modification, and RNA regulation.

DNA Methylation

DNA methylation is the most well-known mechanism of epigenetics. It typically involves a methyltransferase enzyme that assists with the addition of a methyl group on the fifth position of cytosine (C5). This addition occurs mainly on cytosine-phosphate- guanine (CpG) dinucleotides. However, non-CpG methylation occurs as well. Analysis of DNA methylation is often performed to help understand gene expression. Examples of this type of analysis include methylation quantification by digestion of DNA with subsequent analysis through HPLC, mass spectrometry, or using sodium bisulfate conversion followed by PCR sequencing and analysis.

Histone Modification

Histone modification is another classic epigenetic mechanism. It involves various ways of altering histones by acetylation, methylation, phosphorylation, and other mechanisms that affect gene expression. Histones are proteins, that along with DNA, make up nucleosomes. Bundles of nucleosomes create the chromatin that make up chromosomes. In general, histone modifications take place at the histone N-terminal tails with high proportions of the amino acids lysine or arginine. One way to study this epigenetic regulation is through the use of chromatin immunoprecipitation (ChIP) assays.

RNA Regulation

Less is known about RNA regulation than the other epigenetic mechanisms. RNA signaling is thought to play a role in epigenetics through regulating chromatin structure. Researchers are investigating how mRNA and specifically non-coding RNA, such as long non-coding RNA, and micro RNA regulate gene expression. Additionally, Chromatin isolation by RNA purification (ChIRP) or RNA immunoprecipitation (RIP) assays can be used to understand the relationship between chromatin and RNA and the role RNA has in epigenetics.

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  • Cancer research has revealed that the classical model of carcinogenesis, a three step process consisting of initiation, promotion, and progression, is not complete.
  • Frequently ask questions about ChIP.
  • There are several common ways to determine whether a gene contains methylated DNA. Since mammalian methylation occurs at cytosines, researchers take advantage of the fact that methylated cytosine (meC) is stable to bisulfite treatment but unmethylated cytosine is transformed to uracil under the same conditions.
  • Epigenetics is a term coined to describe changes that are not mutation based but can still be passed on from generation to generation. Genes that are activated or repressed without any change in DNA sequence are epigenetically controlled. Epigenetic modifications are stable, but potentially reversible alterations in gene expression that occur without permanent changes in DNA sequence.
  • The overall degree of methylation of a genome can be a useful measure of global regulatory changes. Measurement of this parameter is usually performed after complete digestion to the single base and then analyzed using HPLC or mass spectrophotometry. The Global DNA Modification Kit (MDQ1), allows the researcher to monitor DNA methylation using a format similar to a sandwich ELISA assay.
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