Australian Dental Journal

The official journal of the Australian Dental Association

Australian Dental Journal 2014; 59:(1 Suppl): 23–33

doi: 10.1111/adj.12155

Epigenetics: a new frontier in dentistry

SD Williams,* TE Hughes,* CJ Adler,† AH Brook,*‡ GC Townsend*
*School of Dentistry, The University of Adelaide, South Australia, Australia.
†Institute of Dental Research, Westmead Millennium Institute, Faculty of Dentistry, The University of Sydney, New South Wales, Australia.
‡Institute of Dentistry, Queen Mary University of London, United Kingdom.

ABSTRACT
In 2007, only four years after the completion of the Human Genome Project, the journal Science announced that epige-
netics was the ‘breakthrough of the year’. Time magazine placed it second in the top 10 discoveries of 2009. While our
genetic code (i.e. our DNA) contains all of the information to produce the elements we require to function, our epige-
netic code determines when and where genes in the genetic code are expressed. Without the epigenetic code, the genetic
code is like an orchestra without a conductor. Although there is now a substantial amount of published research on epi-
genetics in medicine and biology, epigenetics in dental research is in its infancy. However, epigenetics promises to
become increasingly relevant to dentistry because of the role it plays in gene expression during development and subse-
quently potentially influencing oral disease susceptibility. This paper provides a review of the field of epigenetics aimed
specifically at oral health professionals. It defines epigenetics, addresses the underlying concepts and provides details
about specific epigenetic molecular mechanisms. Further, we discuss some of the key areas where epigenetics is impli-
cated, and review the literature on epigenetics research in dentistry, including its relevance to clinical disciplines. This
review considers some implications of epigenetics for the future of dental practice, including a ‘personalized medicine’
approach to the management of common oral diseases.
Keywords: Epigenetics, methylation, acetylation, oral health, dentistry.
Abbreviations and acronyms: CLP = cleft lip/cleft palate; mRNA = messenger RNA; ncRNA = non-coding ribonucleic acid; ORF =
open reading format; SSC = squamous cell carcinoma.

‘At the heart of this new field is a simple contentious

INTRODUCTION
idea – that genes have a “memory”. That the lives of
Despite the completion of the Human Genome Project your grandparents – the air they breathed, the food
in 2003, establishing causal relationships between spe- they ate, even the things they saw – can directly affect
cific genes and complex diseases has proved challen- you, decades later, despite your never experiencing
ging.1 As a consequence, the focus of researchers has these things yourself.’4
shifted to identifying how variation in gene expression Two specific layers of information are encoded
influences the development of disease. The field of epi- within the human genome, conferred by discrete
genetics interrogates the molecular mechanisms that chemical structures. The first, and most well-known
link the genetic code and the environment, and the layer, contains our genetic code that is encoded within
molecular mechanisms themselves are referred to as the nucleotide sequence and base pairs of a double
epigenetic mechanisms. Epigenetic mechanisms have helix of deoxy-ribonucleic acid (DNA). Our genetic
now been implicated in many disease processes and in code contains all of the information to produce the
a surprising number of other areas, including newer elements we require to function, but it does not con-
research that suggests epigenetics could also explain tain the ‘programme’ that determines when and where
intergenerational disease susceptibility not directly genes are expressed; this is encoded within the second
hardwired into our genetic material.2 Evidence is layer. The second layer of information contains an
emerging that epigenetic alterations, including DNA epigenetic code for development and maintenance that
methylation and histone modifications, are transmit- dictates when and where various genes are activated
ted transgenerationally, providing a potential mecha- and deactivated during embryogenesis, growth and
nism for environmental influences on parents to be throughout life. It is this epigenetic code that allows
passed to their children.3 A BBC science programme our genetically-identical cells to express different
has summarized these exciting discoveries as follows: patterns of genes. So, rather than having trillions of
© 2014 Australian Dental Association 23
SD Williams et al.

cloned cells doing the same thing, we have distinct code which usually does not change over time and is
cell populations with different phenotypes and func- identical in 99% of the cells in the body. Epigenetic
tions working together to form different tissues that, modifications have been shown to be responsible for
in turn, form the organs that allow us to live. Figure 1 our developmental programme, turning genes on and
provides a visual metaphor that likens our genetic off at precise moments during embryonic develop-
code to an orchestra, with the sheet music being the ment. When cells are differentiating, taking on spe-
epigenetic code, the conductor being the epigenetic cialized roles, methylation helps switch off genes that
machinery, the orchestra members and their instru- are not needed. Furthermore, some epigenetic modifi-
ments the genes, and the combined resulting sounds cations are stable and can be inherited from cell cycle
representing the phenotype. to cell cycle and from parents (possibly even grand-
The epigenetic code works through chemical modifi- parents) to children.6–8 For example, the experiences
cations of the genetic code at different ‘levels’. This of a parent, even before conceiving, can markedly
includes modifications of the linear structure of DNA influence the structure and function of the nervous
itself (DNA methylation), as well as modifications of system in subsequent generations. Using olfactory
structural complexes around which DNA is packaged molecular specificity in mice, Dias and Ressler9 show
(histone protein acetylation in nucleosomes), and also parental experience influencing behaviour and neural
by elaboration of extra-genetic non-coding ribonucleic structure in subsequent generations.
acids (ncRNAs). Many epigenetic modifications affect Epigenetic modifications of the genetic code are
genetic expression by switching genes on or off and caused by environmental stimuli and hence are
preventing messenger RNA (mRNA) formation, or by responsible for our ability to adapt to different envi-
affecting protein structure after translation from an ronments. This adaptation is not limited to physical
mRNA template. In either case, the mechanism affects adaptations but is also relevant to emotional adapta-
protein production and so affects genetic expression. tions; this includes how we respond to stressful situa-
These modifications can work in isolation, but tend to tions or emotional trauma. For this reason,
work in concert, especially methylation and histone- epigenetics is now seen as the missing piece of the
protein acetylation.5 Epigenetic modifications change puzzle, linking the environment to phenotype. As
with time and are tissue specific, unlike the genetic such, much research is now focusing on epigenetics to
try to explain differences in phenotype that cannot be
explained by conventional genetics.1,10,11 A simple
way to look at this is to ask why so-called (geneti-
cally) identical twins do not ever look truly identical;
or to ask why a certain population is more susceptible
to a certain disease.12–15 When our epigenetic code
runs awry, it causes problems and these changes have
been implicated in many disease states and patholo-
gies, including cancers, inflammatory diseases, autoim-
mune diseases and suicide.16,17
This paper provides a review of the field of epigenet-
ics that is aimed specifically at oral health professionals.
It considers different definitions of the term ‘epigenet-
ics’ and ‘environment’, links epigenetics and the envi-
ronment, addresses the underlying concepts, provides
some details about specific epigenetic molecular mecha-
nisms, discusses some of the key areas where epigenet-
ics is implicated, and also reviews some of the recent
literature on epigenetics research in dentistry. It also
considers some implications for the future of dental
practice, including a ‘personalized medicine’ approach
Fig. 1 The Music of Life. Conceptually, our genetic code is like an to the management of common oral diseases.
orchestra with a group of musicians and their different instruments capa-
ble of producing notes and whole melodies independently. However,
without sheet music and someone to interpret the music and conduct the DEFINING EPIGENETICS
orchestra, the musicians are more than likely to produce a cacophony
rather than a symphony! In this analogy, the sheet music is the epige- Epigenetics is not easily defined. More recently formed
netic code, the conductor is the epigenetic machinery instructing the definitions, while accurate, do not indicate the true
musicians (who are equivalent to individual genes) when to play the
notes and how to play them. The resultant sound is equivalent to a scope of epigenetics, whereas the original definition,
phenotype and, with any luck, is pleasing to the ear. which is still applicable, does not provide any molecu-
24 © 2014 Australian Dental Association
 Epigenetics: a new frontier in dentistry

lar detail. As such, the history of epigenetics needs to

THE ENVIRONMENT AND GENETIC REGULATION
be considered when discussing any current definition.
The term epigenetics was first coined by Conrad In line with our definition of epigenetics, we also want
Waddington in 1942, some 11 years before the struc- to clarify what is meant by ‘environmental factors’
ture of DNA was described by Watson and Crick in acting upon the genome. Environmental factors have
1953.18 Epigenetics can be split as ‘epi-’ and ‘-genetics’. been shown to up- and down-regulate genetic expres-
The term genetics is well-understood but defining ‘epi’ sion.22 However, the definition of what constitutes an
is not so simple. As a prepositional prefix it means ‘environmental factor’ is changeable. As technology
‘on, upon, or above’ and most modern applications has improved, explanations of what is referred to as
take this definition. In this respect, epigenetics refers ‘environmental’ have become more specific. For
to something acting upon the genome. Whilst modern instance, Darwin’s theory of evolution described the
technology has shown that epigenetic mechanisms do macroscopic environment in which a plant or animal
in fact occur ‘upon the genome’, and Waddington rec- exists as affecting their evolution; similarly, cigarette
ognized that something must be acting on the genome smoke might be seen as an environmental factor that
in order to regulate it, his definition takes ‘epi’ as an contributes to certain disease states.
apocopation of epigenesis and provides a broader We know that our cells exist within a microscopic
insight. Epigenesis refers to ‘development’; that is, the environment and that the products of one cell can influ-
development of a complex being from a totipotent ence other cells. However, it is now appreciated that
stem cell (Fig. 2) and Waddington’s definition points our genetic material exists within a nanoscale environ-
to this as follows, ‘… interactions … which bring[s] ment and that molecules can also interact with our
the phenotype into being’. Implicit in this definition DNA. Regardless of the scale, ‘the environment’ has
are the temporal and spatial components of epigenetics usually been invoked as the culprit to account for phe-
that modern research is only just describing, over half notypic differences that cannot be attributed to differ-
a century after it was coined by Waddington.18–21 ential genetic expression. Ultimately, however, any
Taking these different perspectives into account, we factor that confers a change in phenotype must do so
propose that an acceptable working definition of epi- by differentially affecting genetic expression at the
genetics could be: a group of acquired or inherited molecular level.
and potentially transgenerational dynamic molecular Socioeconomic status is linked to health disparities,
mechanisms that are affected by the environment and including oral health. Epigenetic changes are a poten-
act directly upon the genome and genetic machinery tial mechanism contributing to these changes. The
throughout life to regulate gene expression. findings from a large community based study in the
USA suggest that the DNA methylation is socially
patterned.23

EPIGENETIC MOLECULAR MECHANISMS

It is currently understood that environmentally
induced epigenetic regulation of gene activity occurs
by one of two methods, either by affecting chromatin
condensation (DNA methylation and histone protein
modification), or by preventing protein production
directly (non-coding RNA).16,24–27 This section will
discuss the general structure of the human genome to
provide a context for later sections, which discuss the
specifics of the different epigenetic modifications.
The 23 pairs of human chromosomes are comprised
Fig. 2 Waddington’s Epigenetic Landscape. Waddington’s epigenetic of varying continuous lengths of double-stranded lin-
landscape is a metaphor for how gene regulation modulates development. ear DNA that are wrapped around structural proteins
Imagine a number of marbles rolling down a hill towards a wall. The
marbles will compete for the grooves on the slope, and the ridges (histone proteins) and then further coiled and super-
between the grooves represent the increasing irreversibility of cell type coiled. Stretched end to end, human DNA is 2 m long,
differentiation. Each marble will come to rest at the lowest possible but it is condensed into a nucleus that might only be
point, representing eventual cell fates, or tissue types. This concept has
been more formalized in the context of a systems dynamics state 0.5 lm in diameter. Due to the condensation required
approach to the study of cell-fate,79 which has opened the door to the for chromosomes to be packaged into a nucleus, the
key role played by stochastic fluctuation (cellular noise), as well as phys- genes on a chromosome are normally inaccessible for
ical fields, in both cell differentiation and cell proliferation. Further dis-
cussion of dynamic systems theory can be found in the paper by Brook transcription and ultimately protein production; local
and colleagues in this special issue. sections of the strand must be ‘unwound’ in order to
© 2014 Australian Dental Association 25
SD Williams et al.

provide access for transcription factors and the than chance predicts. Furthermore, CpGs tend to
machinery required to commence transcription. The occur in clusters so that when they do occur, they are
genetic material in the nucleus is variably packaged in vastly over-represented in these areas. These clusters
different densities, reflecting the level of active tran- of CpGs are known as CpG islands and they tend to
scription. The less densely packed material, euchroma- occur in the promoter regions of genes. Studies have
tin, is relatively uncondensed and allows for active shown that although these CpGs do not relate directly
transcription of the coding regions in the uncondensed to a gene when compared with CpG islands in gene
areas. The more densely packed material, heterochro- promoters, they are associated with many disease
matin, is too condensed to allow transcription activat- states.32,33 Hypermethylation of CpG islands results
ing factors to bind to promoters on the strand to start in inhibition of gene transcription in the area, and
transcription. Epigenetic mechanisms influence the hypomethylation results in activation of these genes;
level of chromatin condensation, and therefore the variation in DNA methylation occurs at specific genes
amount of genetic transcription. but can also show a trend across the entire genome.34
Epigenetic mechanisms have been found to affect
both coding and non-coding regions of the genome.
Histone modification
The coding regions account for 2% of the length of
our DNA and contain approximately 20 000 genes (in Histone proteins form the core proteinaceous struc-
coding regions)28 that, when spliced during post-trans- ture around which DNA is wrapped; the histone pro-
lational modification, are capable of producing tein along with its associated part of the DNA strand
approximately 200 000 proteins. It was originally form nucleosomes. The structure of the nucleosome
thought that the remaining non-coding regions con- determines how the DNA further condenses and this
tained only space-filling junk DNA. However, ultimately affects genetic expression. The most com-
research has shown that these regions are likely to be mon form of histone modification is acetylation of its
crucial for gene regulation and the structural integrity eight subunits, which are referred to as octamers.35
of the strand; we know they are fundamental for epi- Similar to hypo- and hypermethylation, both hyper-
genetic modifications. Epigenetic mechanisms act not and hypoacetylation can affect chromatin condensation
only in the coding regions of our genetic material but and allow or prevent gene transcription respectively,
also in the non-coding regions, as altering the struc- although the mechanisms are different. Like DNA
ture of the structural (non-coding) parts of the DNA methylation, histone acetylation is also associated with
affects the remainder of the DNA.29,30 both site-specific and genome-wide chromatin structure
and therefore gene transcription. Histone acetylation is
also associated with DNA synthesis and damage repair.
DNA methylation
Further, like methylation, histone modifications are
Each DNA strand is comprised of a sequence of four heritable and survive DNA replication.36,37
nucleotides: adenine (A), thymine (T), guanine (G) and
cytosine (C). Specific nucleotides on one strand are
DNA methylation and histone acetylation interaction
always paired with those of the opposite: A with T, and
G with C. There are approximately equal numbers of DNA methylation is a chemical modification of the
each nucleotide in the whole genome. DNA methyla- DNA itself, whereas histone protein modifications are
tion is a covalent modification of cytosine in the DNA. chemical modifications of one of the key proteins
It occurs by the addition of a methyl group to a cytosine around which DNA wraps. Both exert a major influ-
residue on the linear DNA strand; however, methyla- ence on chromatin structure, and therefore gene
tion only occurs where cytosine is adjacent to guanine. expression. Despite both acting in different regions
It is important to differentiate between C being adja- and using different enzymes, there is likely a reflexive
cent to G (in the case of a CpG group/dinucleotide) on relationship between these two systems. Indeed, recent
the same strand, rather than opposite G (as in the case research has demonstrated that the enzymes from the
of C-G base pairing) on the opposing strand. This dis- two systems may interact directly.5
tinction is significant because adjacent Cs and Gs form The interrelationship between DNA methylation
a palindrome once complimentary base pairing occurs. and histone protein modification is particularly impor-
This allows methyl groups to survive DNA replication tant for somatic cell reprogramming and stem cell
and is fundamental for methylome stability; this is research. During development, pluripotent stem cells
important for all models of transgenerational inheri- lose their potency and eventually become terminally
tance as it allows the genetic programme to survive differentiated. This process is tightly regulated and
from one cell generation to the next.31 involves a complex interplay between DNA methyla-
CpGs are under-represented in the genome: they tion and histone protein modification. It is important
occur throughout the genome but are less frequent because the process can be reversed so that somatic
26 © 2014 Australian Dental Association
 Epigenetics: a new frontier in dentistry

cells can be reprogrammed back to a pluripotent frame (ORF) and are translated to proteins, whereas
state.38 Figure 3 illustrates the physical and chemical non-coding RNAs (ncRNAs) do not possess an ORF
relationships between DNA and the two primary epi- and do not elaborate proteins; however, whilst ncR-
genetic mechanisms. NAs do not elaborate an active element (protein), they
are themselves active.
It is now estimated that only 2–5% of RNA codes for
Non-coding RNA
proteins, either structural or enzymatic. The remaining
RNA is the coding unit from which proteins are pro- 95% of RNA is non-coding. Of this 95%, most is used
duced. DNA is transcribed into RNA and RNA is as the machinery for the 2–5% of RNA that does code
translated into proteins. Unlike DNA, RNA is single for proteins (e.g. transport-RNA and ribosomal-RNA).
stranded. RNA contains the same nucleotides as The remaining ncRNAs regulate the levels of mRNA
DNA, aside from uracil (U) that is substituted for thy- and are considered to be part of the ‘epigenetic’ soup.39
mine (T). The similarity between the nucleotides in More recent analysis of the data from the human
RNA and DNA allows them to share a complemen- genome project is showing that although the number
tary ‘language’. of protein coding genes in the human genome has
The two complementary strands of DNA in the remained largely unchanged, there could be around
double-helix are separated during transcription so that 20 000 ‘dead genes’ hidden in the genome. It is thought
one of the strands of DNA can be transcribed to form that these genes do not code protein, but that the RNA
a single strand of messenger RNA (mRNA). mRNA is generated by them exerts significant effects on the
one of several types of eukaryotic RNA (Table 1). expression of protein coding genes.40
Broadly, RNA can be divided into coding and non- RNA regulation of gene expression can occur by
coding RNA. Coding RNAs possess an open reading preventing transcription of RNA from DNA or by
destroying mRNAs after they are produced. Either
way, protein production and therefore gene expression
are affected.

EXAMPLES FROM BIOLOGY AND MEDICINE

Genetic imprinting
Genetic imprinting is a phenomenon where either the
paternally- or the maternally-inherited gene is
repressed and only the other is transcribed, whereas
usually either gene copy can be transcribed. This
means that for some genes to be active, they must be
inherited from a specific parent. Therefore, imprinted
genes act very differently to non-imprinted genes.
DNA methylation profiles can survive mitosis and
have been implicated as the molecular mastermind
behind the process in which imprinted genes are faith-
fully reproduced in all daughter cells. It is thought
that about 100 out of our 20 000 genes are imprinted.
Fig. 3 The physical and chemical relationships between DNA and the
two primary epigenetic mechanisms – methylation and acetylation. The This number is probably conservative, with more
template for construction and coordination of the ~200 000 structural and imprinted genes being discovered, and even with such
functional proteins in the human body is encoded in genes, which are a small number, their effects are profound.41–43
comprised of double-stranded DNA and arranged in specific groups on
chromosomes within the nucleus of almost all cells. Template informa- Silencing of genes via imprinting has been found to
tion is encapsulated in the nucleic acid code of the DNA. DNA itself is have significant phenotypic effects. Prader–Willi and
a long, linear macromolecule that is packaged with histone proteins to Angelman syndromes were the first disorders discov-
form nucleosomes, and then coiled to form a chromatin strand. Chroma-
tin is further super-coiled and arranged into chromosomes to conserve ered to be associated with imprinting. Both are associ-
nuclear space. In periods of active genetic expression in a cell, the DNA ated with the loss of a specific chromosomal region
is uncoiled locally to enable access of transcriptionally important on chromosome 15 from one parent and silencing of
enzymes to the relevant gene(s).
Epigenetic regulation of DNA transcription within a specific cell or tissue the other copy due to sex-specific imprinting. If the
acts at two levels of DNA organization: by control of histone acetylation loss of this chromosomal region is paternally inher-
regulating enzymatic access, and by methylation of specific cytosine ited, then Prader–Willi syndrome results as a conse-
nucleic acids in the DNA regulating mRNA transcription. Further epige-
netic regulation by microRNA action on messenger RNA occurs post- quence of the silencing of the paternally-derived
transcriptionally. SNRPN and necdin genes, along with clusters of genes
© 2014 Australian Dental Association 27
SD Williams et al.

Table 1. Types and functions of eukaryotic RNA

RNA type Function

Coding (relative abundance 3%)

Messenger RNA Transcribed from template DNA; carries encoded nucleic acid message from nucleus to extra-nuclear sites of
protein manufacture (ribosomes); nucleic acid code is read (triplet codon) and translated into an amino acid
sequence to produce a polypeptide chain (protein).
Non-coding (relative abundance 97%)
Transfer RNA Small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at
the ribosomal site of protein synthesis during translation; has sites for amino acid attachment and an anticodon
region for codon recognition that binds to a specific sequence on the messenger RNA chain; complementary base
pairing of triplet nucleotide sequence provides specificity.
Ribosomal RNA This is the catalytic component of the ribosomes. In the cytoplasm, ribosomal RNA and protein combine to form
a nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Nearly all of the
RNA found in a typical eukaryotic cell is rRNA.
Regulatory
MicroRNA Small chains of 17–25 nucleotides; act through RNA interference (RNAi), where an effector complex of miRNA
and enzymes can cleave complementary mRNA, block the mRNA from being translated, or accelerate its
degradation.
Small, interfering RNA Acts through RNA interference in a fashion similar to micro RNAs; some miRNAs and siRNAs can cause genes
they target to be methylated, thereby decreasing or increasing transcription of those genes.
RNA processing
Small nuclear RNA Involved in modifying other RNAs.
Small nucleolar RNA

coding for a series of small nucleolar RNAs. Patients ences between the most and the least socially privi-
with Prader–Willi syndrome usually display short stat- leged.23
ure, cognitive and behavioural problems, and chronic It is known that certain environmental stressors can
hunger that often leads to obesity. If the loss of the induce changes in the human body. Epigenetics, partic-
chromosomal region is maternally inherited then Ang- ularly methylation, has been shown to provide this link
elman syndrome will result as a consequence of the between the environment and phenotype in many cases.
silencing of the maternally-derived SNRPN gene. For example, intrauterine nutrition can cause epigenetic
Patients with Angelman syndrome show severe cogni- changes via DNA methylation in the foetus. The effects
tive impairment, happy excitable demeanour, and pro- of these changes can be immediately apparent, and
found speech impairment. some changes can persist and render their effects later
in life. Foetal folate deficiency is one such example. If
the mother does not consume enough dietary folate,
Cancer
there is a lack of methyl groups available for the epige-
Much epigenetics research focuses on cancer. In gen- netic machinery. As a result, certain genes do not
eral, cancers present with genome-wide global hypome- become methylated. This also results in chromosomal
thylation and gene-specific hypermethylation. The instability. Both of these epigenetic changes can cause
hypermethylation usually occurs within the promoters birth defects, especially of the neural tube, and are asso-
of tumour suppressor genes and this switches them off ciated with problems such as spina bifida.46,47
(silences them). Histone hypo-acetylation is also impli- Exposure to environmental toxins in occupational
cated in the silencing of tumour suppressor genes. The chemicals, cigarette smoke, contaminated air and
absence of tumour suppressor genes allows for the drinking water, as well as fossil fuel emission, may
uncontrolled growth of cells and hence tumourigenesis. cause epigenetic changes. Diesel fumes, pesticides and
Tumours (malignant or benign) appear in the body arsenic produce distinct patterns that can be identified.
fairly regularly, but the body normally detects and elim- Smoking has a measureable effect on DNA methyla-
inates them quickly if they progress to this stage. Silenc- tion and has been associated with hypermethylation of
ing of the tumour suppressor genes will have drastic tumour suppressor genes.48–50 Research has also
implications, especially when combined with overall shown that the variability in susceptibility to environ-
hypomethylation which results in increased gene mental and dietary toxins between people may be due
expression and therefore cell growth. This relationship to differences in how different individuals metabolize
has been demonstrated in many cancers, including oral and process methyl groups generally. Differences in
squamous cell carcinomas (SCC).44,45 methyl metabolism may result in susceptibility to
epigenetic changes that cause health problems. The
findings of Dias and Ressler9 provide a framework for
Environmental stressors
addressing how environmental information may be
Evidence is emerging that the epigenome is affected inherited transgenerationally at behavioural, neuroan-
by socially patterned factors with epigenetic differ- atomical and epigenetic levels.
28 © 2014 Australian Dental Association
 Epigenetics: a new frontier in dentistry

Methylation and human behaviour a hyperinflammatory response with concomitant peri-

odontal breakdown.
Research is now suggesting that ‘give me the child, I
It is now evident that epigenetic changes in the
will give you the man’ might have a molecular under-
genes encoding cytokines can alter their expression,
pinning whereby ‘nurture’ adjusts DNA methylation
leading to either pro- or anti-inflammatory responses.
patterns, which concomitantly fine-tune genetic
Studies have shown that epigenetic changes of the
expression and therefore phenotype. Experiments in
genes encoding pro-inflammatory cytokines are associ-
rodents have shown a strong link between adversity in
ated with periodontitis.55 Other studies have shown
early life and epigenetic profile in later life. It is hard
an association between epigenetic changes and peri-
to test this in humans as the brain is not accessible for
odontitis.56–58 Most published studies have focused
testing in live subjects. However, studies of suicide
on chronic periodontitis, but a link has also been
victims have shown that those who were abused in
established between DNA methylation of pro-inflam-
early childhood had significantly higher levels of
matory mediator genes and aggressive periodontitis.59
hypermethylation of rRNA genes in neurones, and
One of the most revealing studies has shown a link
therefore produced fewer ribosomes for protein pro-
between periodontitis and HIV-1 and AIDS progres-
duction. Importantly, these changes were specific to
sion.60 Specifically, it was shown that periodontitis
the hippocampus, the part of the brain associated
can reactivate HIV-1 expression through an epigenetic
with memory formation.51–53
mediator. This study not only shows a correlation
between a systemic disease and periodontitis, but also
EXAMPLES FROM DENTISTRY explains at least part of the molecular mechanism
linking the two. The study goes further to suggest
Few articles in the dental literature relate to epigenet- possible future treatment options that have already
ics. However, there are some papers published about received FDA approval in the USA (for treatment of
the role of epigenetics in SSCs, but as cancer was one other conditions). The article mentions two ‘epigenetic
of the original areas of epigenetic research and the therapies’ approved; one involves using suberoylani-
treatment of SSCs is not strictly within the purview of lide hydroxamic acid in the treatment of T-cell lym-
dentists, these studies will not be discussed further phomas, the other involves using DNA methyl
here. Aside from head and neck cancer research, much transferase DNMT inhibitors for the treatment of
epigenetic research in dentistry relates mainly to peri- myelodysplastic syndrome and leukaemia. Unfortu-
odontology and orthodontics. However, it is interest- nately, these treatments are associated with significant
ing to note that these disciplines approach the topic in systemic effects, and no targeted epigenetic therapies
completely different ways, as will be discussed below. have been developed to date. Nevertheless, this
research suggests that targeted therapies could play a
part in the management of HIV-AIDS and, possibly,
Periodontology
periodontitis in the future.
Across any given population people will display varied The epigenetic changes on pro-inflammatory media-
inflammatory and immune responses to a given stimu- tors in periodontal disease have been linked to a num-
lus. Research has shown that much of the variability is ber of environmental stimuli, including smoking and
due to differences in what is a highly complex poly- nutrition, and the oral bacteria themselves. Iacopino61
genic immune system. However, more recent research states that these changes in the host tissues can facili-
is demonstrating that the immune system and inflam- tate bacterial colonization, increase inflammatory
matory responses are highly dependent upon epigenetic damage and also provide bacteria with increased levels
mechanisms to function. This has implications for of carbohydrate for metabolism. He also notes that
all inflammatory diseases, including periodontitis.54 these findings have implications for the methods used
Cytokines are some of the biomolecules constituting to diagnose periodontal disease and to identify patients
the inflammatory response. These substances are small at risk. He suggests that a new approach to manage-
proteins that act as chemical messengers and modulate ment of periodontal problems in the future, based on
the immune response. Broadly, there are pro-inflam- personalized medicine, is likely to consider additional
matory cytokines and anti-inflammatory cytokines. factors apart from bleeding and pocket depths,
The balance of these cytokines determines what including types of bacteria present in the biofilm and
response is taken by the immune system to particular epigenetic changes in the periodontal tissues.61
environmental stimuli. In the case of periodontitis in a
susceptible host, toxins and breakdown products from
Orthodontics
bacteria and immune cells result in a significant pre-
disposition towards a pro-inflammatory cytokine The approach to epigenetics research used in the ortho-
response to these stimuli, causing the development of dontic literature is different to that in the periodontal
© 2014 Australian Dental Association 29
SD Williams et al.

literature. As discussed earlier, the definition of epige- era, he notes that there is an increasing awareness of
netics has changed over time. Although Waddington’s the genes and their products that regulate craniofacial
definition points to some molecular mechanism, earlier development, including the notion that these genes are
usage represents a broader viewpoint. This broader turned on and off at critical times. He states that ‘the
view usually refers to some environmental factor caus- issue is not the fact that intrinsic factors within the
ing a phenotypic change but without reference to any genome regulate morphogenesis, but that the complex
molecular interaction. Over time, usage of the term epi- interaction of cells and tissues with remote extrinsic
genetics began to refer to intracellular chemical envi- factors within the body and the environment are trig-
ronments and now the intra-genomic chemical gers, or switches for gene expression that influences
environment is considered to be the location of epige- postnatal growth and responsiveness to clinical treat-
netic activity. While current periodontal research is ment’. This demonstrates a broader view of epigenet-
interrogating the action of known (molecular) epige- ics, but does not stress that these complex interactions
netic mechanisms on specific genes, the orthodontic lit- result in specific molecular epigenetic changes. Carl-
erature concentrates on the ‘bigger picture’ of son goes on to speculate that ‘Within the next several
epigenetics and tends to categorize environmental fac- decades, orthodontists will be using molecular kits to
tors, such as forces acting on the jaw, as inducing diagnose growth-related problems and to determine
growth or remodelling at the condyle. This use tends to precisely each patient’s developmental status as well
place the environmental factor outside of the genome, as the presence or absence of key polymorphisms for
rather than acting upon it. Forces acting upon the jaw growth factors and signalling molecules’.
may induce epigenetic changes that affect gene expres-
sion, but the orthodontic literature does not currently
Cleft lip/cleft palate
describe which epigenetic modifications are affecting
which genes. It is interesting to note that, in his later For such complex and heterogenous disorders, a
work, Melvin Moss62–65 did distinguish between epige- multifactorial model of inheritance is favoured in
netic processes (e.g. mechanical loading) and the epige- which genetic risk factors interact with environmental
netic processes that enact changes. Moss refers to a co-variates.70 In a genome-wide study when gene-envi-
range of epigenetic processes from the macro environ- ronment models were applied to three common envi-
ment (e.g. joint loading), down to and including specific ronmental exposures in pregnancy, the significant
mention of DNA methylation, albeit, generally.65 interactions found were: MLLT3 and SMC2 with alco-
Proffit notes that the major differences in theories of hol consumption; TBK1 and ZNF236 with maternal
craniofacial growth relate to the location at which the smoking; and BAALC with multivitamin supplementa-
genetic control is thought to be expressed.66 For exam- tion.71,72 Future studies will further elucidate the role
ple, if bone is considered to be a primary determinant of epigenetic factors in cleft lip/cleft palate and provide
of craniofacial growth, it is implied that genetic control a basis for sound preventive advice to reduce the fre-
is expressed at the level of bone. If cartilage is consid- quency of this distressing condition; the dental profes-
ered to be the primary determinant, then genetic con- sion will have a role in providing this advice.
trol is considered to lie at the level of cartilage. If the
soft tissue matrix in which the skeletal elements are
Enamel development and defects
embedded is considered to be the primary determinant
of bone, as described in Moss’s Functional Matrix The clinical aspects of this topic are covered in the
Hypothesis,61–65,67 then genetic control is assumed to paper by Seow elsewhere in this issue.73 Here we note
reside outside the skeletal system. It is this indirect the influence of DNA methylation on the enamel pro-
genetic control that is referred to as ‘epigenetic’ in the tein, amelogenin, produced from genes on the X and
orthodontic literature, with changes in bone or carti- Y chromosomes. In the somatic cells of females one
lage occurring in response to signals from other tissues, of the two X chromosomes is ‘inactivated’. However,
i.e. epigenetic controls. The concept of ‘epigenetic while most genes on that chromosome are inactivated,
orthodontics’ that is often equated to ‘functional ortho- approximately 15% escape to some degree and a fur-
dontics’ has developed from this broader view of epige- ther 10% show variable patterns of inactivation.
netics, with spurious explanations put forward such as DNA methylation is involved in this X-chromosome
‘epigenetic orthodontics uses a person’s natural genes inactivation, genetic imprinting and tissue gene
to correct and straighten the teeth and jaws using expression.74,75
biomimetic DNA appliances’.68
Carlson has reviewed the various theories and con-
Behaviour management problems
cepts of craniofacial growth and development and
related them to the developments in the field of genet- It has long been established that maternal fear of den-
ics.69 In discussing developments in the post-genomic tistry is an important factor in the anxiety and prob-
30 © 2014 Australian Dental Association
 Epigenetics: a new frontier in dentistry

lems that some children experience in accepting dental research is demonstrating that epigenetic therapy might
treatment.76 The new evidence of transgenerational one day be an effective treatment for periodontitis.78
transmission of fear at behavioural, neuroanatomical Furthermore, in terms of dental development, it may be
and epigenetic levels6 suggests that, for some anxious possible to intervene early on to prevent hypodontia
children, their dental anxiety may have deeper roots and a range of dental anomalies. In the shorter time
than learned behaviour from the parent. This implies frame though, epigenetics could be used as a reliable
that for some children treatment will need to aim not screening tool for a range of dental anomalies, includ-
only at addressing learned fears but also at seeking ing inherited enamel defects, as well as a means of
epigenetic changes. assessing an individual’s susceptibility to dental caries
Some insights about this come from the paper by and periodontal disease. Exciting times lie ahead!
Yehuda and co-workers77 showing that psychotherapy
constitutes a form of ‘environmental regulation’ that
DISCLOSURE STATEMENT
may alter the epigenetic state. Psychotherapy influenced
the activity of a stress hormone, and altered the methyl- The authors have no conflicts of interest to declare.
ation of a specific region of DNA, the FKBP5 gene. Also
in this study, methylation of the GR gene (NR3C1)
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© 2014 Australian Dental Association 33