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Epigenetics. © INRA, INRA

Livestock epigenetics: laying the foundation for future benefits

Molecular mechanisms involved in epigenetics

Epigenetic tags are chemical additions made either to the DNA or its affiliated proteins, the histones. These tags mediate the expression of the genes upon which they have been placed, either by activating or inhibiting them.

By Pascale Mollier, translated by Jessica Pearce
Updated on 07/10/2014
Published on 05/21/2014

Dividing meristematic root cells in Arabidopsis; depiction of the phragmoplast (double green line). The cytoskeleton is labeled in green (GFP), and the nuclear histones are labeled in red (YFP).. © INRA, BANORA Mohamed Youssef / DE ALMEIDA-ENGLER Ja
Dividing meristematic root cells in Arabidopsis; depiction of the phragmoplast (double green line). The cytoskeleton is labeled in green (GFP), and the nuclear histones are labeled in red (YFP). © INRA, BANORA Mohamed Youssef / DE ALMEIDA-ENGLER Ja

Tagging DNA

The best described form of epigenetic tagging is DNA methylation, a process by which tags are added to cytosines found in one of the following DNA sequences: CG, CHG, or CHH (where H stands for an adenine, thymine, or cytosine and G stands for a guanine; these are the nucleotides that make up DNA). More recently, another mechanism has been discovered: 5-hydroxymethylation.  

In animals, 3 to 8% of cytosines are tagged with methyl groups; this percentage can reach as high as 50% in plants or be as low as zero in yeasts and nematodes. When promoter regions are methylated, gene expression is usually inhibited, while methylation of the gene coding sequences themselves often leads to high levels of expression.

Methyl tags can be retained across cell division cycles, provided that methylases are present and active (see box below). If the methylation pattern is kept in place as the cell divides, then the epigenetic tags present in the mother cell will be passed on to the daughter cells. If not, the methylation pattern is not transmitted. There are also demethylases that actively remove the tags.

Tagging histones

Histones can also be tagged via methylation. In addition, tags can be added to histones by mechanisms such as acetylation, phosphorylation, or ubiquitination. Histones are the proteins around which DNA is coiled; DNA and histones together form the chromatin. Tags placed on histones influence chromatin structure and thus gene expression. When these tags result in chromatin condensation, genes can no longer be accessed by the transcription machinery. Their expression is therefore inhibited. In several types of histones, tags can be added to multiple locations (in particular to the amino acids lysine and methionine). A “histone codebook” has been established to keep track of what different tag combinations signify, as this system of multiple combinations allows very fine-scale regulation of gene expression (see this interview with Hervé Vaucheret).

The result: chromatin structure is changed

Certain other molecules, such as noncoding RNA sequences (which range in size from twenty to several hundreds of thousands of nucleotides), can change the outer structure of DNA, add methyl groups to it, or modify its histones, thus regulating gene expression. There seems to be a certain degree of coordination between the different epigenetic mechanisms to create chromatin regions that demonstrate different levels of transcription, resulting in differential gene expression.

Epigenetic inheritance

As development proceeds, certain tags are added while others are removed, a process whose dynamics depend on both cell type and endogenous and exogenous stimuli. All this is repeated in every generation. Epigenetic modifications are reversible adjustments of gene expression.

However, some research shows that epigenetic tags can be transmitted from one generation to the next. For example, when a mouse is conditioned to associate an odor with an electric shock, the mouse becomes more sensitive to that odor. This physiological response stems from epigenetic modifications of the gene that codes for the receptor for that odor. Furthermore, what we observe is that the mouse’s offspring will demonstrate this same sensitivity to the odor, even though the offspring themselves have not experienced electric shocks (1).

Epigenotypes are therefore “heritable”: when the epigenome of a pregnant female undergoes modifications as a result of environmental changes, her fetus may also be affected, via the placenta, as well as that fetus’s gametes. As a result, three generations may be impacted at the same time.

We use the term epigenetic inheritance to describe epigenetic modifications that are passed on to the next generation, in particular when that generation has not been directly exposed “in utero” or “in testis” to environmental changes.

(1) Reference: Brian G Dias & Kerry J Ressler. Parental olfactory experience influences behavior and neural structure in subsequent generations. December 2013; doi:10.1038/nn.3594

Retaining methyl tags when DNA is duplicated

Several categories of methylases have been described, including enzymes that add new epigenetic tags and enzymes that maintain tags already in place. Maintenance enzymes ensure that methyl tags are retained as DNA is being replicated prior to cell division. Methyl groups on CG sequences are kept in place by an enzyme that recognizes hemimethylated DNA sequences (1). In contrast, enzymes that add new tags are needed to maintain methylation patterns on CHH sequences (2) across cycles of DNA replication. To add a new tag, specific information is required that may be furnished by the complementary RNA of the sequence to be methylated, or it may necessitate the modification of a specific histone. For example, in plants, a chromomethylase that recognizes H3K9me2 tags is responsible for methylating CHG sequences.

(1)    During DNA replication, the palindromic sequences Cmet–G/Cmet–G produce the hemimethylated double-stranded sequences Cmet–G/C–G and C–G/Cmet–G, which are recognized by maintenance enzymes. Palindromic sequences are sequences that are the same whether they are read from 5’ to 3’ on one strand or from 5’ to 3’ on the complementary strand. These enzymes add methyl groups to the non-methylated strand that results from replication, thus restituting the original sequences: Cmet–G/Cmet–G. 

(2)    Cmet–H–H/H–H–G (where H = A, C, or T) sequences contain a single cytosine on a single strand. Replication therefore yields the double-stranded methylated sequence Cmet–H–H/H–H–G and the double-stranded non-methylated sequence C–H–H/H–H–G. Therefore only enzymes that place new tags can ensure that the methylation pattern is restituted on the non-methylated strand.