Epigenetic mechanisms
Epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence. The Greek prefix epi- (ἐπι- "over, outside of, around") in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic basis for inheritance. Epigenetics most often denotes changes that affect gene activity and expression, but can also be used to describe any heritable phenotypic change. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal development. The standard definition of epigenetics requires these alterations to be heritable, either in the progeny of cells or of organisms.
The term also refers to the changes themselves: functionally relevant changes to the genome that do not involve a change in the nucleotide sequence. Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. These epigenetic changes may last through cell divisions
for the duration of the cell's life, and may also last for multiple
generations even though they do not involve changes in the underlying
DNA sequence of the organism; instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently.
One example of an epigenetic change in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. In other words, as a single fertilized egg cell – the zygote – continues to divide, the resulting daughter cells change into all the different cell types in an organism, including neurons, muscle cells, epithelium, endothelium of blood vessels, etc., by activating some genes while inhibiting the expression of others.
Historically, some phenomena not necessarily heritable have also
been described as epigenetic. For example, the term epigenetic has been
used to describe any modification of chromosomal regions, especially
histone modifications, whether or not these changes are heritable or
associated with a phenotype. The consensus definition now requires a
trait to be heritable for it to be considered epigenetic.
Definitions
The term epigenetics in its contemporary usage emerged in the 1990s, but for some years has been used in somewhat variable meanings. A consensus definition of the concept of epigenetic trait
as "stably heritable phenotype resulting from changes in a chromosome
without alterations in the DNA sequence" was formulated at a Cold Spring Harbor meeting in 2008, although alternate definitions that include non-heritable traits are still being used.
Historical
The term epigenesis has a generic meaning "extra growth". It has been used in English since the 17th century.
Waddington's canalisation, 1940s
From the generic meaning, and the associated adjective epigenetic, C. H. Waddington coined the term epigenetics in 1942 as pertaining to epigenesis, in parallel to Valentin Haecker's 'phenogenetics' (Phänogenetik). Epigenesis in the context of the biology of that period referred to the differentiation of cells from their initial totipotent state in embryonic development.
When Waddington coined the term, the physical nature of genes and
their role in heredity was not known; he used it as a conceptual model
of how genes might interact with their surroundings to produce a
phenotype; he used the phrase "epigenetic landscape" as a metaphor for biological development. Waddington held that cell fates were established in development (canalisation) much as a marble rolls down to the point of lowest local elevation.
Waddington suggested visualising increasing irreversibility of
cell type differentiation as ridges rising between the valleys where the
marbles (cells) are travelling. In recent times Waddington's notion of the epigenetic landscape has been rigorously formalized in the context of the systems dynamics state approach to the study of cell-fate.
Cell-fate determination is predicted to exhibit certain dynamics, such
as attractor-convergence (the attractor can be an equilibrium point,
limit cycle or strange attractor) or oscillatory.
Developmental psychology
The term "epigenetic" has also been used in developmental psychology
to describe psychological development as the result of an ongoing,
bi-directional interchange between heredity and the environment.
Interactivist ideas of development have been discussed in various forms
and under various names throughout the 19th and 20th centuries. An
early version was proposed, among the founding statements in embryology, by Karl Ernst von Baer and popularized by Ernst Haeckel. A radical epigenetic view (physiological epigenesis) was developed by Paul Wintrebert. Another variation, probabilistic epigenesis, was presented by Gilbert Gottlieb in 2003.
This view encompasses all of the possible developing factors on an
organism and how they not only influence the organism and each other,
but how the organism also influences its own development.
The developmental psychologist Erik Erikson wrote of an epigenetic principle in his book Identity: Youth and Crisis (1968),
encompassing the notion that we develop through an unfolding of our
personality in predetermined stages, and that our environment and
surrounding culture influence how we progress through these stages. This
biological unfolding in relation to our socio-cultural settings is done
in stages of psychosocial development, where "progress through each stage is in part determined by our success, or lack of success, in all the previous stages."
Contemporary
Robin Holliday
defined epigenetics as "the study of the mechanisms of temporal and
spatial control of gene activity during the development of complex
organisms." Thus epigenetic can be used to describe anything other than DNA sequence that influences the development of an organism.
The more recent usage of the word in science has a stricter definition. It is, as defined by Arthur Riggs and colleagues, "the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence."
The term "epigenetics", however, has been used to describe
processes which have not been demonstrated to be heritable, such as some
forms of histone modification; there are therefore attempts to redefine
it in broader terms that would avoid the constraints of requiring
heritability. For example, Adrian Bird
defined epigenetics as "the structural adaptation of chromosomal
regions so as to register, signal or perpetuate altered activity
states." This definition would be inclusive of transient modifications associated with DNA repair or cell-cycle
phases as well as stable changes maintained across multiple cell
generations, but exclude others such as templating of membrane
architecture and prions
unless they impinge on chromosome function. Such redefinitions however
are not universally accepted and are still subject to dispute. The NIH
"Roadmap Epigenomics Project", ongoing as of 2016, uses the following
definition: "For purposes of this program, epigenetics refers to both
heritable changes in gene activity and expression (in the progeny of
cells or of individuals) and also stable, long-term alterations in the
transcriptional potential of a cell that are not necessarily heritable."
In 2008, a consensus definition of the epigenetic trait, "stably
heritable phenotype resulting from changes in a chromosome without
alterations in the DNA sequence", was made at a Cold Spring Harbor meeting.
The similarity of the word to "genetics" has generated many
parallel usages. The "epigenome" is a parallel to the word "genome",
referring to the overall epigenetic state of a cell, and epigenomics refers to more global analyses of epigenetic changes across the entire genome. The phrase "genetic code" has also been adapted – the "epigenetic code"
has been used to describe the set of epigenetic features that create
different phenotypes in different cells. Taken to its extreme, the
"epigenetic code" could represent the total state of the cell, with the
position of each molecule accounted for in an epigenomic map, a
diagrammatic representation of the gene expression, DNA methylation and
histone modification status of a particular genomic region. More
typically, the term is used in reference to systematic efforts to
measure specific, relevant forms of epigenetic information such as the histone code or DNA methylation patterns.
Molecular basis
Epigenetic
changes modify the activation of certain genes, but not the genetic
code sequence of DNA. The microstructure (not code) of DNA itself or the
associated chromatin
proteins may be modified, causing activation or silencing. This
mechanism enables differentiated cells in a multicellular organism to
express only the genes that are necessary for their own activity.
Epigenetic changes are preserved when cells divide. Most epigenetic
changes only occur within the course of one individual organism's
lifetime; however, these epigenetic changes can be transmitted to the
organism's offspring through a process called transgenerational epigenetic inheritance.
Moreover, if gene inactivation occurs in a sperm or egg cell that
results in fertilization, this epigenetic modification may also be
transferred to the next generation.
Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, DNA methylation reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.
DNA damage
DNA damage can also cause epigenetic changes. DNA damage is very frequent, occurring on average about 60,000 times a day per cell of the human body. These damages are largely repaired, but at the site of a DNA repair, epigenetic changes can remain.
In particular, a double strand break in DNA can initiate unprogrammed
epigenetic gene silencing both by causing DNA methylation as well as by
promoting silencing types of histone modifications (chromatin remodeling
- see next section). In addition, the enzyme Parp1 (poly(ADP)-ribose polymerase) and its product poly(ADP)-ribose (PAR) accumulate at sites of DNA damage as part of a repair process. This accumulation, in turn, directs recruitment and activation of the chromatin remodeling protein ALC1 that can cause nucleosome remodeling. Nucleosome remodeling has been found to cause, for instance, epigenetic silencing of DNA repair gene MLH1. DNA damaging chemicals, such as benzene, hydroquinone, styrene, carbon tetrachloride and trichloroethylene, cause considerable hypomethylation of DNA, some through the activation of oxidative stress pathways.
Foods are known to alter the epigenetics of rats on different diets. Some food components epigenetically increase the levels of DNA repair enzymes such as MGMT and MLH1 and p53. Other food components can reduce DNA damage, such as soy isoflavones.
In one study, markers for oxidative stress, such as modified
nucleotides that can result from DNA damage, were decreased by a 3-week
diet supplemented with soy. A decrease in oxidative DNA damage was also observed 2 h after consumption of anthocyanin-rich bilberry (Vaccinium myrtillius L.) pomace extract.
Techniques used to study epigenetics
Epigenetic research uses a wide range of molecular biological techniques to further understanding of epigenetic phenomena, including chromatin immunoprecipitation (together with its large-scale variants ChIP-on-chip and ChIP-Seq), fluorescent in situ hybridization, methylation-sensitive restriction enzymes, DNA adenine methyltransferase identification (DamID) and bisulfite sequencing. Furthermore, the use of bioinformatics methods has a role in (computational epigenetics).
Mechanisms
Several types of epigenetic inheritance systems may play a role in what has become known as cell memory, note however that not all of these are universally accepted to be examples of epigenetics.
Covalent modifications
Covalent
modifications of either DNA (e.g. cytosine methylation and
hydroxymethylation) or of histone proteins (e.g. lysine acetylation,
lysine and arginine methylation, serine and threonine phosphorylation,
and lysine ubiquitination and sumoylation) play central roles in many
types of epigenetic inheritance. Therefore, the word "epigenetics" is
sometimes used as a synonym for these processes. However, this can be
misleading. Chromatin remodeling is not always inherited, and not all
epigenetic inheritance involves chromatin remodeling.
DNA associates with histone proteins to form chromatin.
Because the phenotype of a cell or individual is affected by which of its genes are transcribed, heritable transcription states can give rise to epigenetic effects. There are several layers of regulation of gene expression. One way that genes are regulated is through the remodeling of chromatin. Chromatin is the complex of DNA and the histone
proteins with which it associates. If the way that DNA is wrapped
around the histones changes, gene expression can change as well.
Chromatin remodeling is accomplished through two main mechanisms:
- The first way is post translational modification of the amino acids that make up histone proteins. Histone proteins are made up of long chains of amino acids. If the amino acids that are in the chain are changed, the shape of the histone might be modified. DNA is not completely unwound during replication. It is possible, then, that the modified histones may be carried into each new copy of the DNA. Once there, these histones may act as templates, initiating the surrounding new histones to be shaped in the new manner. By altering the shape of the histones around them, these modified histones would ensure that a lineage-specific transcription program is maintained after cell division.
- The second way is the addition of methyl groups to the DNA, mostly at CpG sites, to convert cytosine to 5-methylcytosine. 5-Methylcytosine performs much like a regular cytosine, pairing with a guanine in double-stranded DNA. However, some areas of the genome are methylated more heavily than others, and highly methylated areas tend to be less transcriptionally active, through a mechanism not fully understood. Methylation of cytosines can also persist from the germ line of one of the parents into the zygote, marking the chromosome as being inherited from one parent or the other (genetic imprinting).
Mechanisms of heritability of histone state are not well understood;
however, much is known about the mechanism of heritability of DNA
methylation state during cell division and differentiation. Heritability
of methylation state depends on certain enzymes (such as DNMT1)
that have a higher affinity for 5-methylcytosine than for cytosine. If
this enzyme reaches a "hemimethylated" portion of DNA (where
5-methylcytosine is in only one of the two DNA strands) the enzyme will
methylate the other half.
Although histone modifications occur throughout the entire
sequence, the unstructured N-termini of histones (called histone tails)
are particularly highly modified. These modifications include acetylation, methylation, ubiquitylation, phosphorylation, sumoylation,
ribosylation and citrullination. Acetylation is the most highly studied
of these modifications. For example, acetylation of the K14 and K9 lysines of the tail of histone H3 by histone acetyltransferase enzymes (HATs) is generally related to transcriptional competence.
One mode of thinking is that this tendency of acetylation to be
associated with "active" transcription is biophysical in nature. Because
it normally has a positively charged nitrogen at its end, lysine can
bind the negatively charged phosphates of the DNA backbone. The
acetylation event converts the positively charged amine group on the
side chain into a neutral amide linkage. This removes the positive
charge, thus loosening the DNA from the histone. When this occurs,
complexes like SWI/SNF
and other transcriptional factors can bind to the DNA and allow
transcription to occur. This is the "cis" model of epigenetic function.
In other words, changes to the histone tails have a direct effect on the
DNA itself.
Another model of epigenetic function is the "trans" model. In
this model, changes to the histone tails act indirectly on the DNA. For
example, lysine acetylation may create a binding site for
chromatin-modifying enzymes (or transcription machinery as well). This
chromatin remodeler can then cause changes to the state of the
chromatin. Indeed, a bromodomain – a protein domain that specifically
binds acetyl-lysine – is found in many enzymes that help activate
transcription, including the SWI/SNF complex. It may be that acetylation acts in this and the previous way to aid in transcriptional activation.
The idea that modifications act as docking modules for related factors is borne out by histone methylation
as well. Methylation of lysine 9 of histone H3 has long been associated
with constitutively transcriptionally silent chromatin (constitutive heterochromatin).
It has been determined that a chromodomain (a domain that specifically
binds methyl-lysine) in the transcriptionally repressive protein HP1
recruits HP1 to K9 methylated regions. One example that seems to refute
this biophysical model for methylation is that tri-methylation of
histone H3 at lysine 4 is strongly associated with (and required for
full) transcriptional activation. Tri-methylation in this case would
introduce a fixed positive charge on the tail.
It has been shown that the histone lysine methyltransferase (KMT)
is responsible for this methylation activity in the pattern of histones
H3 & H4. This enzyme utilizes a catalytically active site called
the SET domain (Suppressor of variegation, Enhancer of zeste,
Trithorax). The SET domain is a 130-amino acid sequence involved in
modulating gene activities. This domain has been demonstrated to bind to
the histone tail and causes the methylation of the histone.
Differing histone modifications are likely to function in
differing ways; acetylation at one position is likely to function
differently from acetylation at another position. Also, multiple
modifications may occur at the same time, and these modifications may
work together to change the behavior of the nucleosome. The idea that multiple dynamic modifications regulate gene transcription in a systematic and reproducible way is called the histone code,
although the idea that histone state can be read linearly as a digital
information carrier has been largely debunked. One of the
best-understood systems that orchestrates chromatin-based silencing is
the SIR protein based silencing of the yeast hidden mating type loci HML and HMR.
DNA methylation frequently occurs in repeated sequences, and helps to suppress the expression and mobility of 'transposable elements': Because 5-methylcytosine can be spontaneously deaminated (replacing nitrogen by oxygen) to thymidine, CpG sites are frequently mutated and become rare in the genome, except at CpG islands
where they remain unmethylated. Epigenetic changes of this type thus
have the potential to direct increased frequencies of permanent genetic
mutation. DNA methylation
patterns are known to be established and modified in response to
environmental factors by a complex interplay of at least three
independent DNA methyltransferases, DNMT1, DNMT3A, and DNMT3B, the loss of any of which is lethal in mice. DNMT1 is the most abundant methyltransferase in somatic cells, localizes to replication foci, has a 10–40-fold preference for hemimethylated DNA and interacts with the proliferating cell nuclear antigen (PCNA).
By preferentially modifying hemimethylated DNA, DNMT1 transfers patterns of methylation to a newly synthesized strand after DNA replication, and therefore is often referred to as the ‘maintenance' methyltransferase. DNMT1 is essential for proper embryonic development, imprinting and X-inactivation.
To emphasize the difference of this molecular mechanism of inheritance
from the canonical Watson-Crick base-pairing mechanism of transmission
of genetic information, the term 'Epigenetic templating' was introduced.
Furthermore, in addition to the maintenance and transmission of
methylated DNA states, the same principle could work in the maintenance
and transmission of histone modifications and even cytoplasmic (structural) heritable states.
Histones H3 and H4 can also be manipulated through demethylation
using histone lysine demethylase (KDM). This recently identified enzyme
has a catalytically active site called the Jumonji domain (JmjC). The
demethylation occurs when JmjC utilizes multiple cofactors to
hydroxylate the methyl group, thereby removing it. JmjC is capable of
demethylating mono-, di-, and tri-methylated substrates.
Chromosomal regions can adopt stable and heritable alternative
states resulting in bistable gene expression without changes to the DNA
sequence. Epigenetic control is often associated with alternative covalent modifications of histones.
The stability and heritability of states of larger chromosomal regions
are suggested to involve positive feedback where modified nucleosomes recruit enzymes that similarly modify nearby nucleosomes. A simplified stochastic model for this type of epigenetics is found here.
It has been suggested that chromatin-based transcriptional regulation could be mediated by the effect of small RNAs. Small interfering RNAs can modulate transcriptional gene expression via epigenetic modulation of targeted promoters.
RNA transcripts
Sometimes
a gene, after being turned on, transcribes a product that (directly or
indirectly) maintains the activity of that gene. For example, Hnf4 and MyoD enhance the transcription of many liver- and muscle-specific genes, respectively, including their own, through the transcription factor activity of the proteins
they encode. RNA signalling includes differential recruitment of a
hierarchy of generic chromatin modifying complexes and DNA
methyltransferases to specific loci by RNAs during differentiation and
development. Other epigenetic changes are mediated by the production of different splice forms of RNA, or by formation of double-stranded RNA (RNAi).
Descendants of the cell in which the gene was turned on will inherit
this activity, even if the original stimulus for gene-activation is no
longer present. These genes are often turned on or off by signal transduction, although in some systems where syncytia or gap junctions are important, RNA may spread directly to other cells or nuclei by diffusion. A large amount of RNA and protein is contributed to the zygote by the mother during oogenesis or via nurse cells, resulting in maternal effect
phenotypes. A smaller quantity of sperm RNA is transmitted from the
father, but there is recent evidence that this epigenetic information
can lead to visible changes in several generations of offspring.
MicroRNAs
MicroRNAs (miRNAs) are members of non-coding RNAs that range in size from 17 to 25 nucleotides. miRNAs regulate a large variety of biological functions in plants and animals. So far, in 2013, about 2000 miRNAs have been discovered in humans and these can be found online in a miRNA database. Each miRNA expressed in a cell may target about 100 to 200 messenger RNAs that it downregulates.
Most of the downregulation of mRNAs occurs by causing the decay of the
targeted mRNA, while some downregulation occurs at the level of
translation into protein.
It appears that about 60% of human protein coding genes are regulated by miRNAs. Many miRNAs are epigenetically regulated. About 50% of miRNA genes are associated with CpG islands, that may be repressed by epigenetic methylation. Transcription from methylated CpG islands is strongly and heritably repressed.
Other miRNAs are epigenetically regulated by either histone
modifications or by combined DNA methylation and histone modification.
mRNA
In 2011, it was demonstrated that the methylation of mRNA plays a critical role in human energy homeostasis. The obesity-associated FTO gene is shown to be able to demethylate N6-methyladenosine in RNA.
sRNAs
sRNAs
are small (50–250 nucleotides), highly structured, non-coding RNA
fragments found in bacteria. They control gene expression including virulence genes in pathogens and are viewed as new targets in the fight against drug-resistant bacteria.
They play an important role in many biological processes, binding to
mRNA and protein targets in prokaryotes. Their phylogenetic analyses,
for example through sRNA–mRNA target interactions or protein binding properties, are used to build comprehensive databases. sRNA-gene maps based on their targets in microbial genomes are also constructed.
Prions
Prions are infectious forms of proteins.
In general, proteins fold into discrete units that perform distinct
cellular functions, but some proteins are also capable of forming an
infectious conformational state known as a prion. Although often viewed
in the context of infectious disease,
prions are more loosely defined by their ability to catalytically
convert other native state versions of the same protein to an infectious
conformational state. It is in this latter sense that they can be
viewed as epigenetic agents capable of inducing a phenotypic change
without a modification of the genome.
Fungal prions
are considered by some to be epigenetic because the infectious
phenotype caused by the prion can be inherited without modification of
the genome. PSI+ and URE3, discovered in yeast in 1965 and 1971, are the two best studied of this type of prion.
Prions can have a phenotypic effect through the sequestration of
protein in aggregates, thereby reducing that protein's activity. In PSI+
cells, the loss of the Sup35 protein (which is involved in termination
of translation) causes ribosomes to have a higher rate of read-through
of stop codons, an effect that results in suppression of nonsense mutations in other genes.
The ability of Sup35 to form prions may be a conserved trait. It could
confer an adaptive advantage by giving cells the ability to switch into a PSI+ state and express dormant genetic features normally terminated by stop codon mutations.
Structural inheritance
In ciliates such as Tetrahymena and Paramecium,
genetically identical cells show heritable differences in the patterns
of ciliary rows on their cell surface. Experimentally altered patterns
can be transmitted to daughter cells. It seems existing structures act
as templates for new structures. The mechanisms of such inheritance are
unclear, but reasons exist to assume that multicellular organisms also
use existing cell structures to assemble new ones.
Nucleosome positioning
Eukaryotic genomes have numerous nucleosomes.
Nucleosome position is not random, and determine the accessibility of
DNA to regulatory proteins. This determines differences in gene
expression and cell differentiation. It has been shown that at least
some nucleosomes are retained in sperm cells (where most but not all
histones are replaced by protamines).
Thus nucleosome positioning is to some degree inheritable. Recent
studies have uncovered connections between nucleosome positioning and
other epigenetic factors, such as DNA methylation and
hydroxymethylation.
Functions and consequences
Development
Developmental
epigenetics can be divided into predetermined and probabilistic
epigenesis. Predetermined epigenesis is a unidirectional movement from
structural development in DNA to the functional maturation of the
protein. "Predetermined" here means that development is scripted and
predictable. Probabilistic epigenesis on the other hand is a
bidirectional structure-function development with experiences and
external molding development.
Somatic epigenetic inheritance, particularly through DNA and histone covalent modifications and nucleosome repositioning, is very important in the development of multicellular eukaryotic organisms.
The genome sequence is static (with some notable exceptions), but cells
differentiate into many different types, which perform different
functions, and respond differently to the environment and intercellular
signalling. Thus, as individuals develop, morphogens
activate or silence genes in an epigenetically heritable fashion,
giving cells a memory. In mammals, most cells terminally differentiate,
with only stem cells retaining the ability to differentiate into several cell types ("totipotency" and "multipotency"). In mammals, some stem cells continue producing new differentiated cells throughout life, such as in neurogenesis,
but mammals are not able to respond to loss of some tissues, for
example, the inability to regenerate limbs, which some other animals are
capable of. Epigenetic modifications regulate the transition from
neural stem cells to glial progenitor cells (for example,
differentiation into oligodendrocytes is regulated by the deacetylation
and methylation of histones.
Unlike animals, plant cells do not terminally differentiate, remaining
totipotent with the ability to give rise to a new individual plant.
While plants do utilise many of the same epigenetic mechanisms as
animals, such as chromatin remodeling,
it has been hypothesised that some kinds of plant cells do not use or
require "cellular memories", resetting their gene expression patterns
using positional information from the environment and surrounding cells
to determine their fate.
Epigenetic changes can occur in response to environmental
exposure – for example, mice given some dietary supplements have
epigenetic changes affecting expression of the agouti gene, which affects their fur color, weight, and propensity to develop cancer.
Controversial results from one study suggested that traumatic
experiences might produce an epigenetic signal that is capable of being
passed to future generations. Mice were trained, using foot shocks, to
fear a cherry blossom odor. The investigators reported that the mouse
offspring had an increased aversion to this specific odor.
They suggested epigenetic changes that increase gene expression, rather
than in DNA itself, in a gene, M71, that governs the functioning of an
odor receptor in the nose that responds specifically to this cherry
blossom smell. There were physical changes that correlated with
olfactory (smell) function in the brains of the trained mice and their
descendants. Several criticisms were reported, including the study's low
statistical power as evidence of some irregularity such as bias in
reporting results.
Due to limits of sample size, there is a probability that an effect
will not be demonstrated to within statistical significance even if it
exists. The criticism suggested that the probability that all the
experiments reported would show positive results if an identical
protocol was followed, assuming the claimed effects exist, is merely
0.4%. The authors also did not indicate which mice were siblings, and
treated all of the mice as statistically independent.
The original researchers pointed out negative results in the paper's
appendix that the criticism omitted in its calculations, and undertook
to track which mice were siblings in the future.
Transgenerational
Epigenetic mechanisms were a necessary part of the evolutionary origin of cell differentiation.
Although epigenetics in multicellular organisms is generally thought to
be a mechanism involved in differentiation, with epigenetic patterns
"reset" when organisms reproduce, there have been some observations of
transgenerational epigenetic inheritance (e.g., the phenomenon of paramutation observed in maize).
Although most of these multigenerational epigenetic traits are
gradually lost over several generations, the possibility remains that
multigenerational epigenetics could be another aspect to evolution and
adaptation.
As mentioned above, some define epigenetics as heritable.
A sequestered germ line or Weismann barrier is specific to animals, and epigenetic inheritance is more common in plants and microbes. Eva Jablonka, Marion J. Lamb and Étienne Danchin have argued that these effects may require enhancements to the standard conceptual framework of the modern synthesis and have called for an extended evolutionary synthesis. Other evolutionary biologists, such as John Maynard Smith, have incorporated epigenetic inheritance into population genetics models or are openly skeptical of the extended evolutionary synthesis (Michael Lynch). Thomas Dickins and Qazi Rahman
state that epigenetic mechanisms such as DNA methylation and histone
modification are genetically inherited under the control of natural selection and therefore fit under the earlier "modern synthesis".
Two important ways in which epigenetic inheritance can be
different from traditional genetic inheritance, with important
consequences for evolution, are that rates of epimutation can be much
faster than rates of mutation and the epimutations are more easily reversible. In plants, heritable DNA methylation mutations are 100,000 times more likely to occur compared to DNA mutations. An epigenetically inherited element such as the PSI+
system can act as a "stop-gap", good enough for short-term adaptation
that allows the lineage to survive for long enough for mutation and/or
recombination to genetically assimilate the adaptive phenotypic change. The existence of this possibility increases the evolvability of a species.
More than 100 cases of transgenerational epigenetic inheritance phenomena have been reported in a wide range of organisms, including prokaryotes, plants, and animals. For instance, mourning cloak butterflies will change color through hormone changes in response to experimentation of varying temperatures.
The filamentous fungus Neurospora crassa is a prominent
model system for understanding the control and function of cytosine
methylation. In this organism, DNA methylation is associated with relics
of a genome defense system called RIP (repeat-induced point mutation)
and silences gene expression by inhibiting transcription elongation.
The yeast prion
PSI is generated by a conformational change of a translation
termination factor, which is then inherited by daughter cells. This can
provide a survival advantage under adverse conditions. This is an
example of epigenetic regulation enabling unicellular organisms to
respond rapidly to environmental stress. Prions can be viewed as
epigenetic agents capable of inducing a phenotypic change without
modification of the genome.
Direct detection of epigenetic marks in microorganisms is possible with single molecule real time sequencing, in which polymerase sensitivity allows for measuring methylation and other modifications as a DNA molecule is being sequenced. Several projects have demonstrated the ability to collect genome-wide epigenetic data in bacteria.
Epigenetics in bacteria
Escherichia coli bacteria
While epigenetics is of fundamental importance in eukaryotes, especially metazoans,
it plays a different role in bacteria. Most importantly, eukaryotes use
epigenetic mechanisms primarily to regulate gene expression which
bacteria rarely do. However, bacteria make widespread use of
postreplicative DNA methylation for the epigenetic control of
DNA-protein interactions. Bacteria also use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation is important in bacteria virulence in organisms such as Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria,
adenine methylation provides signals for DNA replication, chromosome
segregation, mismatch repair, packaging of bacteriophage, transposase
activity and regulation of gene expression. There exists a genetic switch controlling Streptococcus pneumoniae
(the pneumococcus) that allows the bacterium to randomly change its
characteristics into six alternative states that could pave the way to
improved vaccines. Each form is randomly generated by a phase variable
methylation system. The ability of the pneumococcus to cause deadly
infections is different in each of these six states. Similar systems
exist in other bacterial genera.
Medicine
Epigenetics has many and varied potential medical applications.
In 2008, the National Institutes of Health announced that $190 million
had been earmarked for epigenetics research over the next five years. In
announcing the funding, government officials noted that epigenetics has
the potential to explain mechanisms of aging, human development, and
the origins of cancer, heart disease, mental illness, as well as several
other conditions. Some investigators, like Randy Jirtle,
PhD, of Duke University Medical Center, think epigenetics may
ultimately turn out to have a greater role in disease than genetics.
Twins
Direct
comparisons of identical twins constitute an optimal model for
interrogating environmental epigenetics. In the case of humans with
different environmental exposures, monozygotic (identical) twins were
epigenetically indistinguishable during their early years, while older
twins had remarkable differences in the overall content and genomic
distribution of 5-methylcytosine DNA and histone acetylation.
The twin pairs who had spent less of their lifetime together and/or had
greater differences in their medical histories were those who showed
the largest differences in their levels of 5-methylcytosine DNA and
acetylation of histones H3 and H4.
Dizygotic (fraternal) and monozygotic (identical) twins show evidence of epigenetic influence in humans.
DNA sequence differences that would be abundant in a singleton-based
study do not interfere with the analysis. Environmental differences can
produce long-term epigenetic effects, and different developmental
monozygotic twin subtypes may be different with respect to their
susceptibility to be discordant from an epigenetic point of view.
A high-throughput study, which denotes technology that looks at
extensive genetic markers, focused on epigenetic differences between
monozygotic twins to compare global and locus-specific changes in DNA
methylation and histone modifications in a sample of 40 monozygotic twin
pairs.
In this case, only healthy twin pairs were studied, but a wide range of
ages was represented, between 3 and 74 years. One of the major
conclusions from this study was that there is an age-dependent
accumulation of epigenetic differences between the two siblings of twin
pairs. This accumulation suggests the existence of epigenetic “drift”.
Epigenetic drift is the term given to epigenetic modifications as they
occur as a direct function with age. While age is a known risk factor
for many diseases, age-related methylation
has been found to occur differentially at specific sites along the
genome. Over time, this can result in measurable differences between
biological and chronological age. Epigenetic changes have been found to
be reflective of lifestyle and may act as functional biomarkers of
disease before clinical threshold is reached.
A more recent study, where 114 monozygotic twins and 80 dizygotic
twins were analyzed for the DNA methylation status of around 6000
unique genomic regions, concluded that epigenetic similarity at the time
of blastocyst splitting may also contribute to phenotypic similarities
in monozygotic co-twins. This supports the notion that microenvironment
at early stages of embryonic development can be quite important for the
establishment of epigenetic marks.
Congenital genetic disease is well understood and it is clear that epigenetics can play a role, for example, in the case of Angelman syndrome and Prader-Willi syndrome.
These are normal genetic diseases caused by gene deletions or
inactivation of the genes, but are unusually common because individuals
are essentially hemizygous because of genomic imprinting,
and therefore a single gene knock out is sufficient to cause the
disease, where most cases would require both copies to be knocked out.
Genomic imprinting
Some human disorders are associated with genomic imprinting,
a phenomenon in mammals where the father and mother contribute
different epigenetic patterns for specific genomic loci in their germ cells. The best-known case of imprinting in human disorders is that of Angelman syndrome and Prader-Willi syndrome – both can be produced by the same genetic mutation, chromosome 15q partial deletion,
and the particular syndrome that will develop depends on whether the
mutation is inherited from the child's mother or from their father. This is due to the presence of genomic imprinting in the region. Beckwith-Wiedemann syndrome
is also associated with genomic imprinting, often caused by
abnormalities in maternal genomic imprinting of a region on chromosome
11.
Rett syndrome is underlain by mutations in the MECP2 gene despite no large-scale changes in expression of MeCP2 being found in microarray analyses. BDNF is downregulated in the MECP2 mutant resulting in Rett syndrome.
In the Överkalix study, paternal (but not maternal) grandsons
of Swedish men who were exposed during preadolescence to famine in the
19th century were less likely to die of cardiovascular disease. If food
was plentiful, then diabetes mortality in the grandchildren increased, suggesting that this was a transgenerational epigenetic inheritance.
The opposite effect was observed for females – the paternal (but not
maternal) granddaughters of women who experienced famine while in the
womb (and therefore while their eggs were being formed) lived shorter
lives on average.
Cancer
A variety of epigenetic mechanisms can be perturbed in different
types of cancer. Epigenetic alterations of DNA repair genes or cell
cycle control genes are very frequent in sporadic (non-germ line)
cancers, being significantly more common than germ line (familial) mutations in these sporadic cancers.
Epigenetic alterations are important in cellular transformation to
cancer, and their manipulation holds great promise for cancer
prevention, detection, and therapy.
Several medications which have epigenetic impact are used in several of
these diseases. These aspects of epigenetics are addressed in cancer epigenetics.
Diabetic wound healing
Epigenetic
modifications have given insight into the understanding of the
pathophysiology of different disease conditions. Though, they are
strongly associated with cancer, their role in other pathological
conditions are of equal importance. It appears that, the hyperglycaemic
environment could imprint such changes at the genomic level, that
macrophages are primed towards a pro-inflammatory
state and could fail to exhibit any phenotypic alteration towards the
pro-healing type. This phenomenon of altered Macrophage Polarization is
mostly associated with all the diabetic complications in a clinical
set-up. At present, several reports reveal the relevance of different
epigenetic modifications with respect to diabetic complications. Sooner
or later, with the advancements in biomedical
tools, the detection of such biomarkers as prognostic and diagnostic
tools in patients could possibly emerge out as alternative approaches.
It is noteworthy to mention here that the use of epigenetic
modifications as therapeutic targets warrant extensive preclinical as
well as clinical evaluation prior to use.
Psychology and psychiatry
Early life stress
In
a groundbreaking 2003 report, Caspi and colleagues demonstrated that in
a robust cohort of over one-thousand subjects assessed multiple times
from preschool to adulthood, subjects who carried one or two copies of
the short allele of the serotonin transporter promoter polymorphism
exhibited higher rates of adult depression and suicidality when exposed
to childhood maltreatment when compared to long allele homozygotes with
equal ELS exposure.
Parental nutrition, in utero exposure to stress, male-induced
maternal effects such as attraction of differential mate quality, and
maternal as well as paternal age, and offspring gender could all
possibly influence whether a germline epimutation is ultimately
expressed in offspring and the degree to which intergenerational
inheritance remains stable throughout posterity.
Addiction
Addiction is a disorder of the brain's reward system which arises through transcriptional
and neuroepigenetic mechanisms and occurs over time from chronically
high levels of exposure to an addictive stimulus (e.g., morphine,
cocaine, sexual intercourse, gambling, etc.). Transgenerational epigenetic inheritance of addictive phenotypes has been noted to occur in preclinical studies.
Anxiety
Transgenerational epigenetic inheritance of anxiety-related phenotypes has been reported in a preclinical study using mice.
In this investigation, transmission of paternal stress-induced traits
across generations involved small non-coding RNA signals transmitted via
the male germline.
Depression
Epigenetic inheritance of depression-related phenotypes has also been reported in a preclinical study.
Inheritance of paternal stress-induced traits across generations
involved small non-coding RNA signals transmitted via the paternal
germline.
Fear conditioning
Studies
on mice have shown that certain conditional fears can be inherited from
either parent. In one example, mice were conditioned to fear a strong
scent, acetophenone,
by accompanying the smell with an electric shock. Consequently, the
mice learned to fear the scent of acetophenone alone. It was discovered
that this fear could be passed down to the mice offspring. Despite the
offspring never experiencing the electric shock themselves the mice
still displayed a fear of the acetophenone scent, because they inherited
the fear epigenetically by site-specific DNA methylation. These
epigenetic changes lasted up to two generations without reintroducing
the shock.
Research
The
two forms of heritable information, namely genetic and epigenetic, are
collectively denoted as dual inheritance. Members of the APOBEC/AID
family of cytosine deaminases
may concurrently influence genetic and epigenetic inheritance using
similar molecular mechanisms, and may be a point of crosstalk between
these conceptually compartmentalized processes.
Fluoroquinolone antibiotics induce epigenetic changes in mammalian cells through iron chelation. This leads to epigenetic effects through inhibition of α-ketoglutarate-dependent dioxygenases that require iron as a co-factor.
Various pharmacological agents are applied for the production of
induced pluripotent stem cells (iPSC) or maintain the embryonic stem
cell (ESC) phenotypic via epigenetic approach. Adult stem cells like
bone marrow stem cells have also shown a potential to differentiate into
cardiac competent cells when treated with G9a histone methyltransferase
inhibitor BIX01294.
Pseudoscience
Due to epigenetics being in the early stages of development as a science and the sensationalism surrounding it in the public media, David Gorski and geneticist Adam Rutherford advised caution against proliferation of false and pseudoscientific conclusions by new age authors who make unfounded suggestions that a person's genes and health can be manipulated by mind control. Misuse of the scientific term by quack authors has produced misinformation to the general public.
