Epigenetics Book: The Most Comprehensive Exploration of the Practical, Social and Ethical Impact of DNA on Our Society and Our World
By Roy Carroll
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Epigenetics Book - Roy Carroll
Table of Contents
Chapter One
Chapter Two
Chapter Three
Chapter Four
Chapter Five
Chapter Six
Chapter Seven
Chapter Eight
Epigenetics Book
The Most Comprehensive
Exploration of the Practical, Social
and Ethical Impact of DNA on Our
Society and Our World
Roy Carroll
Copyright All rights reserved.
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Chapter One
About Epigenetics
In biology, epigenetics is the study
of heritable phenotype changes that do not involve alterations in the DNA sequence. The Greek prefix epi- 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 involves changes that affect gene activity and expression, but the term 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 in the progeny of either cells or 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.
The term epigenetics in its contemporary usage emerged in the 1990s, but for some years has been used with somewhat variable meanings. A consensus definition of the concept of epigenetic trait as a "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.
The term epigenesis has a generic meaning of extra growth
, and has been used in English since the 17th century.
Developmental psychology
In a somewhat different context to its usage in biological sciences, the word epigenetic
has often been used in developmental psychology to define psychological growth as a product of a constant, bi-directional interaction between heredity and the environment. Interactive theories about creation have been explored in numerous ways and under multiple titles in the 19th and 20th centuries. An early edition, among the founding statements of embryology, was suggested by Karl Ernst von Baer and popularized by Ernst Haeckel. Paul Wintrebert has developed a progressive epigenetic dream (physiological epigenesis). Another form, probabilistic epigenesis, was described in 2003 by Gilbert Gottlieb. This perspective covers all potential evolutionary effects on the organism and how they affect not just the organism and each other, but also how the organism affects its own growth.
Erik Erik Erikson, a developmental psychologist, wrote about the epigenetic concept in his 1968 book Identity: Youth and Crisis, which incorporates the idea that we grow through the evolution of our personalities in fixed phases, and that our atmosphere and underlying society affect how we advance through these phases. This biological evolution in relation to our socio-cultural environments takes place at the level of psychosocial progression, where progress in each level is partially decided by our performance or lack of success in all previous stages.
While empiric experiments have produced varying findings, epigenetic changes are believed to be a biological trigger for transgenerational trauma.
Molecular basis
Epigenetic shifts affect the function of other genes, but not the DNA gene code chain. The microstructure (not the code) of DNA itself or the related chromatin proteins can be changed, resulting in activation or silencing. This process enables segregated cells in a multicellular organism to produce only the genes required for their own activity. Epigenetic variations are retained as the cells separate. Some epigenetic modifications arise only over the lifespan of an adult organism; nevertheless, these epigenetic changes may be passed to the descendants of the organism by a mechanism called transgenerational epigenetic inheritance. In fact, if gene inactivation happens in a
sperm or egg cell that results in fertilization, this epigenetic alteration can often be passed to the next generation.
Different epigenetic mechanisms include paramuting, bookmarking, imprinting, gene silencing, X-chromosome inactivation, positioning influence, reprogramming of DNA methylation, transvection, maternal results, advancement in carcinogenesis, a broad variety of teratogenic effects, histone and heterochromatin control, and technological constraints concerning parthenogenesis and cloning.
DNA damage
DNA damage may also induce epigenetic changes.[25][26][27]
DNA damage is very normal, occurring on average around 60,000 times a day per human body cell (see DNA damage (naturally occurring). These damages are mostly remedied, but epigenetic modifications can remain at the DNA repair site. In particular, a double-stranded DNA split will cause unprogrammed epigenetic gene silencing both by inducing DNA methylation and by facilitating the silencing of histone alteration forms (Chromatin remodeling-see next section). In addition, the enzyme Parp1 (poly(ADP)-ribose polymerase) and its component poly(ADP)-ribose (PAR) accumulate at DNA damage sites as part of the repair phase. Such aggregation, in effect, drives recruitment and activation of the ALC1 chromatin remodeling protein that may induce nucleosome remodeling.
Nucleosome remodeling has been shown to induce, for example,
epigenetic silencing of the MLH1 DNA repair gene. DNA harmful chemicals, such as benzene, hydroquinone, styrene, carbon tetrachloride and trichloroethylene, cause considerable hypomethylation of DNA, some through the triggering of oxidative stress pathways.
Foods are known to change the epigenetics of rats in various diets. Some food components epigenetically raise the amount of DNA repair enzymes, such as MGMT and MLH1 and p53. Other food components, such as soy isoflavones, may reduce DNA damage. In one test, oxidative stress indicators, such as changed nucleotides that may result from DNA injury, were reduced by a 3-week diet complemented with soy. Decreased oxidative DNA damage was also detected 2 h after anthocyanin-rich bilberry (Vaccinium myrtillius L.) extract of pomace was eaten.
Techniques used to study epigenetics
Epigenetic work utilizes a broad variety of molecular biological methods to better explain epigenetic processes, including chromatin immunoprecipitation (together with its large-scale versions ChIP-on-chip and ChIP-Seq), fluorescent in situ hybridization, methylation-sensitive restriction enzymes, DNA adenine methyltransferase recognition (DamID) and bisulphite sequencing. In fact, the application of bioinformatics has a role to play in statistical epigenetics.
Mechanisms Some