Table Of ContentEpigenetics and Epigenomics
Edited by Christopher J. Payne
Epigenetics and Epigenomics
Edited by Christopher J. Payne
D3pZ4i & bhgvld, Dennixxx & rosea (for softarchive)
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Published by AvE4EvA
Copyright © 2014
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Published 29 April, 2014
ISBN-10 9535113631
ISBN-13 978-9535113638
C ontents
Preface
Chapter 1 Epigenetic Mechanisms of the Vascular Endothelium
by Alexandra A. Majerski, Anthony C. Quinton and
Philip A. M arsden
Chapter 2 Epigenetics, Prote in Kinases and Heart Failure
by Richard M. Millis, M. Sadegh Asadi, Vernon Bond, Jr.
and Georges E. Haddad
Chapter 3 Current Understanding of Epigenomics and Epigenetics
in Neurod evelopmental Disorders
by Takeo Kubota, Kunio Miyake and Takae Hirasawa
Chapter 4 Epigenetic Mechanisms in Autism Spectrum Disorders
by Tafari Mbadiwe and Richard M. Millis
Chapter 5 Geno mic Imprinting and Human Reproduction
by I.N. Lebedev
Chapter 6 Methylomes
by Minghua Wu
Chapter 7 Epigenome, Cancer Prevention and Flavonoids and
Curcumin
by Viÿnja Stepanic, Renata Novak Kujundÿic and
Koraljka Gall Troÿelj
Preface
The book aims to provide an overview of current knowledge regarding
epigenetics and epigenomics.
Included are reviews on the role of epigenetics in the development
and pathogenesis of the vascular endothelium and nervous system, as
well as our current understanding of the potential etiologies of
Autism Spectrum Disorders. A
dditional chapters are devoted to DNA methylation, genomic imprinting
and human reproduction. A discussion of the role of the epigenome in
cancer prevention and polyphenols is also included.
Authors provide research findings from both human data and animal
model studies.
This book will be of interest to scientists, physicians and lay
readers wishing to review recent developments in the field of
epigenetics and epigenomics.
Chapter 1
Epigenetic Mechanisms of the Vascular Endothelium
Alexandra A. Majerski, Anthony C. Quinton and
Philip A. Marsden
Additional information is available at the end of the chapter
http://dx.doi.org/10.5772/58569
1. Introduction
In the same way that Watson and Crick’s breakthrough in identifying the molecular structure
of the DNA double helix revolutionized the last sixty years of molecular biology, the field of
epigenetics is set to do the same for the next sixty (or more) years! An alphabet of four letters,
and strict guidelines dictating their arrangement, comprise the genome of all known living
organisms. This same system has allowed us to unravel many of the secrets to human health
and to comprehend a great number of once-elusive conditions and diseases. Nevertheless, a
vast number of puzzles remain to be solved, and the genetic code is but one tool used to make
sense of them.
Our understanding of our genetics has grown enormously over the last several decades and
the iconic image of the DNA double helix has become a cornerstone for the field. Most certainly,
the information contained within this static DNA code is but a starting point. Yet, a number
of seemingly straightforward questions cannot be answered without going beyond the highly
conserved script. Undoubtedly, many ask: Why and how is an endothelial cell different from
a brain cell when the static DNA genome is identical? To answer this and many other complex
and fascinating phenomena, we must, instead, go over or above (epi-) genetics because the
DNA blueprint is identical in each of the abovementioned somatic cells. A term coined in the
1940s by Conrad Waddington, epigenetics refers to chromatin-based mechanisms important
in the regulation of gene expression that do not involve changes to the DNA sequence per se.
Epigenetic principles, in eukaryotic organisms, are linked by an important common thread:
DNA does not exist in a “naked” state. Figure 1 provides a visual representation of the added
layer of chemical species, as well as proteins which themselves can be modified – all of which
contribute to a layer of chemical complexity and significant implications that epigenetics
strives to classify and understand.
2 Epigenetics and Epigenomics
Division and differentiation are fundamental processes for sending cells of common origin to
different destinations. Logically, the timing and regulation of these processes must be de‐
pendent on more than an identical code contained in all body cells. Thus, the epigenome
comprises the ever-expanding repertoire of chemical alterations that regulate the expression
of genes and, hence, dictate the function of cells and the role of proteins. A number of genetic
determinants, as well as lineage-specific markings, and environmental responses are used to
construct the epigenome [1]. The existence of an epigenetic code is a highly contested topic [2]
and one which will be explored throughout this chapter. Indeed, it is not only mistakes in the
genetic code, but also deviations in the epigenome that may provide clues to understanding
the onset of detrimental conditions and diseases.
2. Three mechanisms of epigenetics
2.1. Posttranslational histone modifications
Compaction of the entire 6 billion base pair genome, 3 billion in each copy of the haploid
genome, into each one of 50 trillion human body cells is a truly breathtaking achievement! In
each cell, 2 meters of DNA are condensed by at least 10, 000 fold in order to fit into the roughly
6 µm diameter of the nucleus. In accomplishing this monumental feat, intricate folding and
wrapping are the first steps in organizing the DNA. Covalent and non-covalent interactions
further alter the three-dimensional arrangement of the chromatin. Chromatin refers to the state
of DNA when it is spooled around the fundamental repeat unit: the nucleosome [3]. Each
nucleosome consists of an octamer containing four different core histone units: histones H2A,
H2B, H3 and H4. Two of each core histone unit are present within one nucleosome such that
a tetramer of H3 and H4 joins two dimers of H2A and H2B [3]. At least one fifth of the amino
acids in each core protein are lysine or arginine – those with highly basic side chains [4].
Approximately 147 base pairs of DNA wrap around each nucleosome. Linker histones,
especially H1, interconnect each nucleosome. Structurally, each of the canonical histone core
proteins has a characteristic N-terminal tail of amino acids extending out from the core, which
is highly susceptible to modifications [3].
Contrary to what biologists believed for many years, kinetic experiments have shown that
DNA wrapping around a nucleosome is surprisingly dynamic. Open exposure for 10 to 50
milliseconds – the length of time between rapid winding and unwinding – means that DNA
is available for binding other proteins [5]. The formation of nucleosomes converts a DNA
molecule into thread-like chromatin approximately one-third of its initial length [4].
Since the initial work in histone acetylation and methylation by Allfrey and colleagues [6],
many other modifications have been documented, with the most frequently found to be, at
steady state, lysine acetylation, mono-, di-, and tri-methylation of lysines, and the phosphor‐
ylation of serines [7]. Concomitantly, a particular collection of enzymes is responsible for each
of these additions: histone acetyl transferases (HATs) and histone methyl transferases (HMTs).
Importantly, each of these modifications are reversible, the opposite reactions catalyzed by a
group of histone deacetylases (HDACs) and histone demethylases (HDMTs). Most often, the
