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It refers to the observed phenotypic variations that are caused by
outer chemical modifications to DNA and/or influenced by a number
of environmental factors that switch genes ‘on’ and ‘off’.
These modifications do not change or alter the DNA sequence,
but instead, they affect how cells ‘read’ specific genes, causing a
difference in gene expression. Epigenetic changes in gene expres-
sion enable an individual plant to respond to changes in the envi-
ronment and regulate the synthesis of required proteins at critical
growth stages.
Epigenetic changes (epigenetic variation) not only influence the ex-
pression of genes in plants, animals and humans, but also enable
the differentiation of stem cells (cells having the potential to become
any type of cells). In other words, epigenetic deviations allow cells
that all share the same DNA, derived from one fertilised embryo to
become specialised cells to form various tissues or complex organs
during normal development. The epigenetic code is cell type and
tissue specific.
Types of epigenetic modifications
In plants there are three main mechanisms for epigenetic gene
regulation, i.e. DNA methylation, histone modifications and RNA
(non-coding RNAi) interference (
Figure 1
). The full extent to which
epigenetic variation contributes to the overall observed phenotypic
variation remains uncertain.
Once these epigenetic variations are established, these can be trans-
ferred from generation to generation (passed on to offspring) in the
form of epigenetic alleles (or alleles having the same DNA sequence
but different DNA methylation patterns) or epimutations.
DNA methylation
DNA methylation is the addition of a methyl group at the fifth carbon
position of a cytosine ring within the DNA sequence. This process is
carried out by a family of naturally occurring DNA methyltransferase
enzymes. DNA methylation is now suggested to be of great evolu-
tionary importance in many species and is extensively associated
with gene silencing (
Figure 2
).
DNA methylation is critical for proper plant development, defects
thereof can lead to physiological plant defects. Presently, DNA
FOCUS
Seed
Special
methylation is one of the most broadly studied and well-character-
ised epigenetic modifications.
Histone modifications
Histones are proteins that the DNA wraps-coils around in an orga-
nised manner (without histones, DNA would be too long to fit inside
cells). If histones hold the DNA strand tightly, the DNA cannot be
‘read’ by the cell.
Modifications that relax or alter the structure (acetylation, methyla-
tion, and phosphorylation) of the histones can make different coding
regions of the DNA accessible to proteins that ‘read’ genes, resulting
in a difference in gene expression (
Figure 3
).
RNA interference
RNA silencing is a general phenomenon in eukaryotic organisms and
plays important roles in various biological processes, including de-
velopmental regulation, antiviral defence and chromatin remodelling.
In plants, there are three RNA silencing pathways. The first involves
small interfering RNAs (siRNAs) that are processed from dicing/cut-
ting small double-stranded RNAs and the second is where small
RNAs, known as microRNAs (miRNAs) both interfere at the post
translation stage. Pathways 1 and 2 interfere with the normal func-
tioning of messenger RNA (mRNA) resulting in no protein produc-
tion for that particular mRNA molecular (
Figure 4
). The third pathway
involves siRNA – which control directed chromatin modifications,
including DNA and histone methylation before translation.
Applications of epigenetic technologies
It is without a doubt that the potential of epigenetics to contribute to-
wards crop improvement is being recognised by leading epigenetic
scientists, crop researchers, large private agricultural companies
and national governments around the world.
Crops can experience a variety of environmental stresses throughout
their full cycle of development, including drought, nutrient toxicities,
flooding and extreme temperatures. Their ability to bear or adapt to
these stresses, as well as their inability to do so, is well documented
in literature and is very complex. However, some recent studies car-
ried out by international research groups, have shown that epige-
netic technologies can be used to effectively down regulate targeted
Figure 2: Transcriptional silencing of gene promoters via DNA methylation.
Maart 2016
38
Epigenetics unlocks
potential