Contents

**Preface XI**

Preface

In "Epigenetics and Epigenomics", leading scientists and clinicians from around the world review the latest findings and current understandings of how epigenetic mechanisms influence the development and physiology of organ systems, how diseases and disorders may arise due to epigenetic dysregula‐ tion, and how the field of epigenomics is increasing our knowledge of biological processes. Most au‐ thors focus on the scientific foundations from which disease states are known to develop, yet whose etiologies are still poorly understood. The book begins with a comprehensive review by Alexandra Ma‐ jerski and colleagues on the epigenetic mechanisms of the vascular endothelium, focusing on the differ‐ ent processes of DNA methylation, histone modifications, and non-coding RNA-mediated events in the context of development and cardiovascular disease. In Chapter 2, Richard Millis and co-authors provide a closer examination of heart failure with respect to protein kinases and their epigenetic regulation. They discuss the current knowledge of how DNA and histone modifications influence cardiomyopathy, detailing the mechanisms that may contribute to this leading cause of mortality worldwide. In Chapter 3, Takeo Kubota and colleagues review the role of epigenomics in the development and onset of neuro‐ developmental disorders, highlighting the contribution of environmental factors, such as malnutrition, chemical and pharmacokinetic side effects, and mental stress. Tafari Mbadiwe and Richard Millis follow up on this subject in Chapter 4, focusing on Autism Spectrum Disorders and the potential effects that epigenetic modulation or dysregulation has on these neurodevelopmental diseases. In Chapter 5, Igor Lebedev provides a review of genomic imprinting and its role in human reproduction. Evidence from clinical studies is presented with a focus on early embryo development and reproductive failures that occur during the first trimester of pregnancy. Minghua Wu reviews the evolution of DNA methylation and its impact on cell differentiation, stem cell reprogramming, tumorigenesis and cancer progression in Chapter 6, including the role of non-coding RNAs in the pathogenesis of gliomas. The book con‐ cludes with a chapter by Višnja Stepanić and co-authors examining polyphenols and their effect on gene expression through the modulation of the epigenome (Chapter 7). The interplay between DNA methyl‐

ation and histone acetylation is discussed in the context of flavonoids and cancer prevention.

These chapters will be useful for scientists, physicians and lay readers wishing to review the current status of knowledge regarding epigenetics and epigenomics. I hope that the chapters will provide inspi‐ ration for new ideas and novel insights of how DNA methylation, histone modifications, and non-cod‐ ing RNA-mediated events influence normal development and physiology and contribute to human disorders and diseases. I sincerely thank all of the authors for their outstanding contributions. I am also grateful to Ms. Iva Lipović for her managerial assistance in the preparation and publication of this book.

**Christopher J. Payne**

Chicago, Illinois, USA

Northwestern University Feinberg School of Medicine,

Ann & Robert H. Lurie Children's Hospital of Chicago Research Center,

## Preface

In "Epigenetics and Epigenomics", leading scientists and clinicians from around the world review the latest findings and current understandings of how epigenetic mechanisms influence the development and physiology of organ systems, how diseases and disorders may arise due to epigenetic dysregula‐ tion, and how the field of epigenomics is increasing our knowledge of biological processes. Most au‐ thors focus on the scientific foundations from which disease states are known to develop, yet whose etiologies are still poorly understood. The book begins with a comprehensive review by Alexandra Ma‐ jerski and colleagues on the epigenetic mechanisms of the vascular endothelium, focusing on the differ‐ ent processes of DNA methylation, histone modifications, and non-coding RNA-mediated events in the context of development and cardiovascular disease. In Chapter 2, Richard Millis and co-authors provide a closer examination of heart failure with respect to protein kinases and their epigenetic regulation. They discuss the current knowledge of how DNA and histone modifications influence cardiomyopathy, detailing the mechanisms that may contribute to this leading cause of mortality worldwide. In Chapter 3, Takeo Kubota and colleagues review the role of epigenomics in the development and onset of neuro‐ developmental disorders, highlighting the contribution of environmental factors, such as malnutrition, chemical and pharmacokinetic side effects, and mental stress. Tafari Mbadiwe and Richard Millis follow up on this subject in Chapter 4, focusing on Autism Spectrum Disorders and the potential effects that epigenetic modulation or dysregulation has on these neurodevelopmental diseases. In Chapter 5, Igor Lebedev provides a review of genomic imprinting and its role in human reproduction. Evidence from clinical studies is presented with a focus on early embryo development and reproductive failures that occur during the first trimester of pregnancy. Minghua Wu reviews the evolution of DNA methylation and its impact on cell differentiation, stem cell reprogramming, tumorigenesis and cancer progression in Chapter 6, including the role of non-coding RNAs in the pathogenesis of gliomas. The book con‐ cludes with a chapter by Višnja Stepanić and co-authors examining polyphenols and their effect on gene expression through the modulation of the epigenome (Chapter 7). The interplay between DNA methyl‐ ation and histone acetylation is discussed in the context of flavonoids and cancer prevention.

These chapters will be useful for scientists, physicians and lay readers wishing to review the current status of knowledge regarding epigenetics and epigenomics. I hope that the chapters will provide inspi‐ ration for new ideas and novel insights of how DNA methylation, histone modifications, and non-cod‐ ing RNA-mediated events influence normal development and physiology and contribute to human disorders and diseases. I sincerely thank all of the authors for their outstanding contributions. I am also grateful to Ms. Iva Lipović for her managerial assistance in the preparation and publication of this book.

> **Christopher J. Payne** Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago Research Center, Chicago, Illinois, USA

**Chapter 1**

**Epigenetic Mechanisms of the Vascular Endothelium**

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

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

> © 2014 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Alexandra A. Majerski, Anthony C. Quinton and

Additional information is available at the end of the chapter

Philip A. Marsden

**1. Introduction**

sense of them.

strives to classify and understand.

http://dx.doi.org/10.5772/58569

## **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.

© 2014 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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].

binding of DNA gene regulatory proteins, or transcription factors, is a pre-requisite for the recruitment action of any of these enzymes. Such events occur at different times in the developmental history of a cell and groups of nucleosomes may be modified in a multitude of

**Figure 1.** Three defining epigenetic mechanisms: DNA methylation, posttranslational histone modifications, and RNAbased mechanisms. The four-lettered (**a**denine, **c**ytosine, **g**uanine, **t**hymine) code that constitutes an individual's ge‐ netic makeup is identical in all cell types and is highly conserved during mitotic and meiotic divisions, whereas the three epigenetic modifications differ amongst cell types and are only partly conserved during mitosis and meiosis. In the "Nurture vs. Nature" debate, genetics characterizes the latter with strong evolutionary convergence while epige‐ netics is influenced by the former, such that the dynamic patterns that classify it diverge rapidly through evolution.

Epigenetic Mechanisms of the Vascular Endothelium

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3

The mechanism by which histone posttranslational modifications (PTMs) occur can be broadly categorized into 3 groups: a) altering chromatin structure with small (acetylation, phosphor‐ ylation, methylation) or large (ubiquitylation, sumoylation) chemical groups, b) inhibiting binding factors to the chromatin, and c) attracting a particular set of proteins to the newly modified regions. In the following, we will highlight the notable features of the well-studied mechanisms and allude to the implications of them throughout the remainder of this chapter.

First, acetylation is a posttranslational histone mark that is known to be correlated with transcriptional activation. Broadly speaking, chromatin structure is loosened by the acetylation of lysine (denoted by K) residues. This modification allows for DNA binding sites to be made more accessible, at the same time that a new collection of proteins are recruited to this region of modified chromatin [8]. Positive charges at highly basic histone tails are neutralized with lysine acetylation, which reduces the binding of the amino acid to the negatively charged DNA [9]. An actual change of the physical properties of the histone tails, such as neutralization, is an example of a *cis*-effect. In this instance, a segmental expansion of the chromatin allows for easier access to transcriptional regulators. When other proteins are actively recruited to the chromatin and read snippets of it, a *trans*-effect is said to occur. The example HPTM recruiting new proteins was observed with histone tail acetylation. Bromodomain are specialized protein

domains, found in HATs such as Gcn5 and CBP/p300. [10, 11].

ways based on the status of the cell [4].

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

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

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

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

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

molecule into thread-like chromatin approximately one-third of its initial length [4].

the onset of detrimental conditions and diseases.

**2. Three mechanisms of epigenetics**

2 Epigenetics and Epigenomics

**2.1. Posttranslational histone modifications**

is highly susceptible to modifications [3].

**Figure 1.** Three defining epigenetic mechanisms: DNA methylation, posttranslational histone modifications, and RNAbased mechanisms. The four-lettered (**a**denine, **c**ytosine, **g**uanine, **t**hymine) code that constitutes an individual's ge‐ netic makeup is identical in all cell types and is highly conserved during mitotic and meiotic divisions, whereas the three epigenetic modifications differ amongst cell types and are only partly conserved during mitosis and meiosis. In the "Nurture vs. Nature" debate, genetics characterizes the latter with strong evolutionary convergence while epige‐ netics is influenced by the former, such that the dynamic patterns that classify it diverge rapidly through evolution.

binding of DNA gene regulatory proteins, or transcription factors, is a pre-requisite for the recruitment action of any of these enzymes. Such events occur at different times in the developmental history of a cell and groups of nucleosomes may be modified in a multitude of ways based on the status of the cell [4].

The mechanism by which histone posttranslational modifications (PTMs) occur can be broadly categorized into 3 groups: a) altering chromatin structure with small (acetylation, phosphor‐ ylation, methylation) or large (ubiquitylation, sumoylation) chemical groups, b) inhibiting binding factors to the chromatin, and c) attracting a particular set of proteins to the newly modified regions. In the following, we will highlight the notable features of the well-studied mechanisms and allude to the implications of them throughout the remainder of this chapter.

First, acetylation is a posttranslational histone mark that is known to be correlated with transcriptional activation. Broadly speaking, chromatin structure is loosened by the acetylation of lysine (denoted by K) residues. This modification allows for DNA binding sites to be made more accessible, at the same time that a new collection of proteins are recruited to this region of modified chromatin [8]. Positive charges at highly basic histone tails are neutralized with lysine acetylation, which reduces the binding of the amino acid to the negatively charged DNA [9]. An actual change of the physical properties of the histone tails, such as neutralization, is an example of a *cis*-effect. In this instance, a segmental expansion of the chromatin allows for easier access to transcriptional regulators. When other proteins are actively recruited to the chromatin and read snippets of it, a *trans*-effect is said to occur. The example HPTM recruiting new proteins was observed with histone tail acetylation. Bromodomain are specialized protein domains, found in HATs such as Gcn5 and CBP/p300. [10, 11].

Histone methylation has proven to be more perplexing than histone acetylation due to the fact that lysine can be mono-, di-, or tri-methylated and arginine can be mono-or di-methylated. Knowing that there are 24 sites of lysine and arginine methylation on the four histone core proteins, means that a tremendous number of methylated/unmethylated states are possible [12-15]. Astonishingly, lysine methylation can result in either the activation or silencing of gene expression. Generally, the methylation of lysines 4, 36, and 79 on histone H3 (H3K4me, H3K36me, H3K79me, respectively) are correlated with transcriptional activation, while the remainder have repressive activity [15]. Two of these marks, namely methylation on lysine 79 of histone H3 and 20 on histone H4, also play a vital role in DNA repair [15]. Arginine methylation is similar, in that the process has been correlated with both negative and positive transcriptional regulation in numerous contexts [16-19].

across the genome shows enrichment at centromeric heterochromatin, repetitive element

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5

Unlike the great variability of histone modifications, DNA methylation is well known to be a mark of transcriptional repression [24]. Having been the first epigenetic mechanism identified, DNA methylation has been studied for the longest time and its consequences are well entrenched in a variety of essential biochemical processes, abnormal conditions, and diseases. X chromosome inactivation and imprinting are two such phenomena where normal DNA methylation in early development plays a vital role in setting the stage for monoallelic expression from chromosones during cellular maturation [25]. Deregulation of the methylation mechanism can lead to Immunodeficiency Centromeric instability, and Facial abnormalities

There are two main hypothesized mechanisms by which DNA methylation is proposed to repress gene expression. The first of these is a physical interference with the binding of regular transcription factors. The methyl group itself may physically project into the major groove of the DNA double helix, whereby it interferes with the sequence-specific recruitment of DNA proteins [27]. In support of this, a number of transcription factors have been found to recognize GC rich regions of the genome – the very same regions that are most susceptible to CpG methylation. Subsequently, these factors are unable to bind when methylcytosine takes the place of cytosine. The second proposed mechanism is in opposition to the first, as proteins are not repelled by the presence of 5mC, but are instead attracted to it. After the purification and cloning of an individual methyl-CpG binding protein, MeCP2 [28], four more similar proteins were identified and are now referred to as methyl-CpG binding domain proteins (MBDs). The attraction of these MBDs has been shown to block the binding of activating transcription factors and to actually recruit to the chromatin, histone-modifying enzymes, chromatin remodelers, and RNA molecules [29-31]. Several such conglomerates have been proposed to co-operatively

The reaction that yields 5mC as its product is catalyzed by a family of three DNA methyl‐ transferases (DNMTs): DNMT1, DNMT3A and DNMT3B [33]. DNMT1, the first of three family members, is a maintenance methyltransferase as it is responsible for transmitting methylation patterns from one cellular generation to the next. Replication of DNA demands that the two strands first be unwound, and it is during this time that DNMT1 is recruited to the replication fork. Binding of proliferating cell nuclear antigen (PCNA) to both strands and UHRF1 (ubiquitin-like with PHD and RING finger domains 1) protein via its characteristic SET-and RING-associated (SRA) domain, are pre-requisites for the recruitment of DNMT1 [34-36]. This enzyme exhibits methylation preference for hemi-methylated DNA, that is, double stranded DNA where only one strand exhibits methylation [37, 38]. Following replication, the parent strand displays the necessary methylation patterns and is subsequently used as a template for the DNMT1-mediated methyl addition to the nascent, naked strand of DNA. Such sites are accurately methylated due to the palindromic nature of the CpG sequences and the fact that methylation patterns between the two strands are symmetrical. Two other DNMTs include

syndrome (ICF) as well as being a contributing factor to cancer progression [26].

(transposon), and non-coding regions [23].

silence gene expression [32].

*2.2.1. DNA methyltransferases*

In contrast to the addition of small chemical species, other larger modifications of histones are described (acetyl, phosphate, and methyl). Ubiquitylation and sumoylation, the addition of ubiquitin (Ub) and small ubiquitin-like modifier (SUMO), respectively, increases the size of the histone by up to two-thirds [20]. Depending on the site of ubiquitylation, this process can result in either transcriptionally active or inactive segments of chromatin [21]. Currently, there are no known ubiquitin chromatin binding proteins, but it is hypothesized that ubiquitin protein is again likely involved in a more diverse array of interactions than are the smaller chemical additions. Although much less well studied, SUMO is thought to recruit deacetylases and/or block lysine substrates that could be acetylated. Both mechanisms are consistent with results that have shown sumoylation to be correlated with transcriptional repression [20].

As a final note on PTMs, chromatin remodelling complexes that rely on the hydrolysis of ATP are known to temporarily alter the structure of nucleosomes by reducing the attraction between DNA and its neighbouring histone. This is commonly referred to as "nucleosome sliding" and the action briefly makes the DNA more susceptible to the effects of other proteins [4]. This sequence of events likely allows for a greater range of interactions of which we are not yet fully aware. It is important to stress that chromatin structure is highly regulated by nucleosome eviction and alternative histone core protein usage. This is a new area of study.

#### **2.2. DNA methylation**

The second major epigenetic pathway is DNA methylation - the addition of a methyl group (- CH3) to the five position of the nitrogenous base, cytosine (Figure 1). Often referred to as the "fifth base pair," the product of this reaction, 5-methylcytosine (5mC), is the most common mutagenic base in the mammalian genome. Mutation of methyl CpG to uracil pG then TpG results in CpG depletion and TpG enrichment in the mammalian genome. DNA methylation is predominantly observed at CpG sites in the mammalian genome, with the methyl modifi‐ cation at non-CpG dinucleotides unusual, except perhaps in stem cells and mature neurons. Not to be confused with cytosine complementarily binding with guanine *across* the DNA double helix, CpG sites refer to locations where cytosine and guanine are separated by a phosphodiester bond, adjacent to one another. The vast majority, approximately 70-80%, of all CpG sites in the mammalian genome are, indeed, methylated [22]. Distribution of methylation across the genome shows enrichment at centromeric heterochromatin, repetitive element (transposon), and non-coding regions [23].

Unlike the great variability of histone modifications, DNA methylation is well known to be a mark of transcriptional repression [24]. Having been the first epigenetic mechanism identified, DNA methylation has been studied for the longest time and its consequences are well entrenched in a variety of essential biochemical processes, abnormal conditions, and diseases. X chromosome inactivation and imprinting are two such phenomena where normal DNA methylation in early development plays a vital role in setting the stage for monoallelic expression from chromosones during cellular maturation [25]. Deregulation of the methylation mechanism can lead to Immunodeficiency Centromeric instability, and Facial abnormalities syndrome (ICF) as well as being a contributing factor to cancer progression [26].

There are two main hypothesized mechanisms by which DNA methylation is proposed to repress gene expression. The first of these is a physical interference with the binding of regular transcription factors. The methyl group itself may physically project into the major groove of the DNA double helix, whereby it interferes with the sequence-specific recruitment of DNA proteins [27]. In support of this, a number of transcription factors have been found to recognize GC rich regions of the genome – the very same regions that are most susceptible to CpG methylation. Subsequently, these factors are unable to bind when methylcytosine takes the place of cytosine. The second proposed mechanism is in opposition to the first, as proteins are not repelled by the presence of 5mC, but are instead attracted to it. After the purification and cloning of an individual methyl-CpG binding protein, MeCP2 [28], four more similar proteins were identified and are now referred to as methyl-CpG binding domain proteins (MBDs). The attraction of these MBDs has been shown to block the binding of activating transcription factors and to actually recruit to the chromatin, histone-modifying enzymes, chromatin remodelers, and RNA molecules [29-31]. Several such conglomerates have been proposed to co-operatively silence gene expression [32].

#### *2.2.1. DNA methyltransferases*

Histone methylation has proven to be more perplexing than histone acetylation due to the fact that lysine can be mono-, di-, or tri-methylated and arginine can be mono-or di-methylated. Knowing that there are 24 sites of lysine and arginine methylation on the four histone core proteins, means that a tremendous number of methylated/unmethylated states are possible [12-15]. Astonishingly, lysine methylation can result in either the activation or silencing of gene expression. Generally, the methylation of lysines 4, 36, and 79 on histone H3 (H3K4me, H3K36me, H3K79me, respectively) are correlated with transcriptional activation, while the remainder have repressive activity [15]. Two of these marks, namely methylation on lysine 79 of histone H3 and 20 on histone H4, also play a vital role in DNA repair [15]. Arginine methylation is similar, in that the process has been correlated with both negative and positive

In contrast to the addition of small chemical species, other larger modifications of histones are described (acetyl, phosphate, and methyl). Ubiquitylation and sumoylation, the addition of ubiquitin (Ub) and small ubiquitin-like modifier (SUMO), respectively, increases the size of the histone by up to two-thirds [20]. Depending on the site of ubiquitylation, this process can result in either transcriptionally active or inactive segments of chromatin [21]. Currently, there are no known ubiquitin chromatin binding proteins, but it is hypothesized that ubiquitin protein is again likely involved in a more diverse array of interactions than are the smaller chemical additions. Although much less well studied, SUMO is thought to recruit deacetylases and/or block lysine substrates that could be acetylated. Both mechanisms are consistent with results that have shown sumoylation to be correlated with transcriptional repression [20].

As a final note on PTMs, chromatin remodelling complexes that rely on the hydrolysis of ATP are known to temporarily alter the structure of nucleosomes by reducing the attraction between DNA and its neighbouring histone. This is commonly referred to as "nucleosome sliding" and the action briefly makes the DNA more susceptible to the effects of other proteins [4]. This sequence of events likely allows for a greater range of interactions of which we are not yet fully aware. It is important to stress that chromatin structure is highly regulated by nucleosome

The second major epigenetic pathway is DNA methylation - the addition of a methyl group (- CH3) to the five position of the nitrogenous base, cytosine (Figure 1). Often referred to as the "fifth base pair," the product of this reaction, 5-methylcytosine (5mC), is the most common mutagenic base in the mammalian genome. Mutation of methyl CpG to uracil pG then TpG results in CpG depletion and TpG enrichment in the mammalian genome. DNA methylation is predominantly observed at CpG sites in the mammalian genome, with the methyl modifi‐ cation at non-CpG dinucleotides unusual, except perhaps in stem cells and mature neurons. Not to be confused with cytosine complementarily binding with guanine *across* the DNA double helix, CpG sites refer to locations where cytosine and guanine are separated by a phosphodiester bond, adjacent to one another. The vast majority, approximately 70-80%, of all CpG sites in the mammalian genome are, indeed, methylated [22]. Distribution of methylation

eviction and alternative histone core protein usage. This is a new area of study.

transcriptional regulation in numerous contexts [16-19].

**2.2. DNA methylation**

4 Epigenetics and Epigenomics

The reaction that yields 5mC as its product is catalyzed by a family of three DNA methyl‐ transferases (DNMTs): DNMT1, DNMT3A and DNMT3B [33]. DNMT1, the first of three family members, is a maintenance methyltransferase as it is responsible for transmitting methylation patterns from one cellular generation to the next. Replication of DNA demands that the two strands first be unwound, and it is during this time that DNMT1 is recruited to the replication fork. Binding of proliferating cell nuclear antigen (PCNA) to both strands and UHRF1 (ubiquitin-like with PHD and RING finger domains 1) protein via its characteristic SET-and RING-associated (SRA) domain, are pre-requisites for the recruitment of DNMT1 [34-36]. This enzyme exhibits methylation preference for hemi-methylated DNA, that is, double stranded DNA where only one strand exhibits methylation [37, 38]. Following replication, the parent strand displays the necessary methylation patterns and is subsequently used as a template for the DNMT1-mediated methyl addition to the nascent, naked strand of DNA. Such sites are accurately methylated due to the palindromic nature of the CpG sequences and the fact that methylation patterns between the two strands are symmetrical. Two other DNMTs include DNMT3A and DNMT3B, both of which have been shown to function as *de novo* methyltrans‐ ferases, displaying preferential methyl addition to unmethylated DNA [39]. These DNMTs play a crucial role in embryonic development, during which time the methylation patterns to be propagated in somatic cells are established [40].

deficiency is a feature of CGI promoters, in general [51-53]. It is not yet known whether this phenomenon is a result of intrinsic chromatin instability or nucleosome exclusion due to the presence of the transcription initiation complex. Interestingly, it was found early in the study of CpG islands that, when found at promoter regions, these segments lack the canonical TATA box that so many eukaryotic promoters possess [54, 55]. Constitutive binding of RNA poly‐ merase II is a frequently documented feature of CGIs. Presence of RNA polymerase II would evidently be associated with transcriptional activation as it is the major player involved in

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http://dx.doi.org/10.5772/58569

7

Several histone chromatin features are also known to typify CpG islands, one of which is the depletion of histone 3 lysine residue 36 dimethylation, H3K36me2 [56]. Even though no conclusion has been reached as to why it is the absence of this dimethylation that characterizes most CpG islands, the modification has been reported, in yeast, to inhibit transcriptional initiation via histone deacetylase attraction. [57-59]. This absence makes way for the transcrip‐ tionally permissive state of CGIs. Furthermore, CGIs are marked by activating histone acetylation; both H3 and H4 acetylation are frequently observed [51, 60]. Notably, Cfp1 (CXXC finger protein 1) is a well characterized and fundamental component of the Setd1 H3K4 methyltransferase complex [61] and is drawn towards the overwhelming majority of CGIs in the mouse genome [62]. In the context of CpG islands, this protein directs H3K4 trimethylation, the activity of which has been shown to prevent DNA methylation of the underlying code [63,

The long-standing study of DNA methylation took a significant turn in 2009 with the redis‐ covery of what is now commonly referred to as the "6th base pair:" 5-hydroxymethylcytosine (5hmC) [65]. This base is the product of an enzymatic reaction that adds a hydroxyl (-OH) group to the methyl of 5-methylcytosine as shown in Figure 2. 5hmC was initially detected in 1972 in mammalian DNA [66], but has since been found primarily, and abundantly, in Purkinje neurons [67], the central nervous system (in the brainstem, spinal cord, and especially the cerebellum [67] and cerebral cortex) [68], and in embryonic stem (ES) cells [65, 69]. The highest tissue levels of 5hmC have been consistently found in the brain [69-71]. The striking abundance of 5hmC in ES cells and PGCs has led scientists to delve into the possibility that 5hmC is linked with the removal of 5mC in such settings, *in vivo*. There is evidence to suggest that, unlike 5mC, 5hmC may be correlated with transcriptional activation, after having been found at euchromatic regions in mice [72, 73]. In essence, while 5mC is known to be a mark of tran‐ scriptional repression, 5hmC may be associated with turning genes back on. Since 2009, a large quantity of research has been generated, dedicated to studying the potential role of 5hmC in gene expression regulation. Despite this, we have only just scratched the surface of discovery

A vital question regarding 5hmC is whether it functions as an intermediate in enzymatic reactions or as a stable entity unto itself. In this chapter, considerable space will be dedicated to discussing the possible demethylation pathways in which 5hmC is speculated to be involved. In this and many contexts, demethylation is defined to be the removal of 5mC and

64]. Hence, the DNA is maintained in a potentially active transcriptional state.

as the role of 5hmC in the genome continues to remain highly elusive.

*2.2.3. 5-hydroxymethylcytosine: the 6th base pair*

regular transcription.

The catalytic domain of the DNA methyltransferases is conserved amongst all of the DNMTs. Despite this, very little similarity is seen at their N-terminal domain. The regulatory domain of DNMT1 is composed of at least five motifs that are not present on the other enzymes, whereas DNMT3A and 3B exhibit two unique motifs. DNMT1 motifs include: a PCNAinteracting domain, a nuclear localization signal, a replication foci-targeting domain, a DNAbinding CXXC region, and a protein-protein interaction motif called the bromo-adjacent homology domain [26]. Those of DNMT3A and 3B include a motif essential for heterochro‐ matin association, PWWP [41, 42] or "pro-trp-trp-pro," as well as a motif for protein-protein interactions: the ATRX-related cysteine-rich region containing a zinc finger and an atypical PHD domain [26].

#### *2.2.2. CpG Islands*

The fact that 5mC is the most common mutagenic base of the mammalian genome can be explained by methylcytosine's susceptibility to deamination [43, 44]. Upon deamination, the modified nitrogenous base is replaced by thymine and a T:G mismatch is generated. Rather than the rapid repair mechanism activated by cytosine deamination to uracil, T:G mismatches tend to accumulate and are not readily removed. Consequently, the genome becomes CpG depleted and TpG enriched. As indicated in Table 1, CpG islands (CGIs) are regions of the genome that have been spared this phenomenon; the number of CpG sites observed (O) is equivalent to the number that would be expected (E) based on C or G nucleotide abundance. As a result, the ideal situation would be an O/E of 1.

The definition of a CpG island has undergone a great deal of revision since the earliest studies dealing with these genomic regions [45] and are now rather arbitrarily defined as being > 500 bp [46], but averaging around 1000 bp. The O/E range determines the strength of a CpG island with the strongest having O/E > 0.75, a weak one with an O/E between 0.45 and 0.75, and a poor CGI having an O/E < 0.45. These regions are characterized by their elevated C+G content with the %C+G content > 55% [46]. These segments are especially fascinating due to their unusually low levels of DNA methylation marks. In essence, these regions are very often observed to be unmethylated. Due to the lack of repressive flags, genes that are downstream of CGI containing promoters are often in an active state of expression. It has been speculated that practically all CGIs are transcription start sites (TSS), largely of housekeeping and developmentally important genes [47, 48]. Approximately 70% of all gene promoters are CGIs [49].

The relationship between structure and function is seen most vividly in many of the compo‐ sitional characteristics of CGIs. For instance, a recent study found that the CGI at the promoters of a particular group of genes was relatively nucleosome-deficient [50]. That is, the underlying DNA was highly accessible to activating transcription factors because less of it was spun around nucleosomes. Evidence from additional studies has shown that this nucleosome deficiency is a feature of CGI promoters, in general [51-53]. It is not yet known whether this phenomenon is a result of intrinsic chromatin instability or nucleosome exclusion due to the presence of the transcription initiation complex. Interestingly, it was found early in the study of CpG islands that, when found at promoter regions, these segments lack the canonical TATA box that so many eukaryotic promoters possess [54, 55]. Constitutive binding of RNA poly‐ merase II is a frequently documented feature of CGIs. Presence of RNA polymerase II would evidently be associated with transcriptional activation as it is the major player involved in regular transcription.

Several histone chromatin features are also known to typify CpG islands, one of which is the depletion of histone 3 lysine residue 36 dimethylation, H3K36me2 [56]. Even though no conclusion has been reached as to why it is the absence of this dimethylation that characterizes most CpG islands, the modification has been reported, in yeast, to inhibit transcriptional initiation via histone deacetylase attraction. [57-59]. This absence makes way for the transcrip‐ tionally permissive state of CGIs. Furthermore, CGIs are marked by activating histone acetylation; both H3 and H4 acetylation are frequently observed [51, 60]. Notably, Cfp1 (CXXC finger protein 1) is a well characterized and fundamental component of the Setd1 H3K4 methyltransferase complex [61] and is drawn towards the overwhelming majority of CGIs in the mouse genome [62]. In the context of CpG islands, this protein directs H3K4 trimethylation, the activity of which has been shown to prevent DNA methylation of the underlying code [63, 64]. Hence, the DNA is maintained in a potentially active transcriptional state.

#### *2.2.3. 5-hydroxymethylcytosine: the 6th base pair*

DNMT3A and DNMT3B, both of which have been shown to function as *de novo* methyltrans‐ ferases, displaying preferential methyl addition to unmethylated DNA [39]. These DNMTs play a crucial role in embryonic development, during which time the methylation patterns to

The catalytic domain of the DNA methyltransferases is conserved amongst all of the DNMTs. Despite this, very little similarity is seen at their N-terminal domain. The regulatory domain of DNMT1 is composed of at least five motifs that are not present on the other enzymes, whereas DNMT3A and 3B exhibit two unique motifs. DNMT1 motifs include: a PCNAinteracting domain, a nuclear localization signal, a replication foci-targeting domain, a DNAbinding CXXC region, and a protein-protein interaction motif called the bromo-adjacent homology domain [26]. Those of DNMT3A and 3B include a motif essential for heterochro‐ matin association, PWWP [41, 42] or "pro-trp-trp-pro," as well as a motif for protein-protein interactions: the ATRX-related cysteine-rich region containing a zinc finger and an atypical

The fact that 5mC is the most common mutagenic base of the mammalian genome can be explained by methylcytosine's susceptibility to deamination [43, 44]. Upon deamination, the modified nitrogenous base is replaced by thymine and a T:G mismatch is generated. Rather than the rapid repair mechanism activated by cytosine deamination to uracil, T:G mismatches tend to accumulate and are not readily removed. Consequently, the genome becomes CpG depleted and TpG enriched. As indicated in Table 1, CpG islands (CGIs) are regions of the genome that have been spared this phenomenon; the number of CpG sites observed (O) is equivalent to the number that would be expected (E) based on C or G nucleotide abundance.

The definition of a CpG island has undergone a great deal of revision since the earliest studies dealing with these genomic regions [45] and are now rather arbitrarily defined as being > 500 bp [46], but averaging around 1000 bp. The O/E range determines the strength of a CpG island with the strongest having O/E > 0.75, a weak one with an O/E between 0.45 and 0.75, and a poor CGI having an O/E < 0.45. These regions are characterized by their elevated C+G content with the %C+G content > 55% [46]. These segments are especially fascinating due to their unusually low levels of DNA methylation marks. In essence, these regions are very often observed to be unmethylated. Due to the lack of repressive flags, genes that are downstream of CGI containing promoters are often in an active state of expression. It has been speculated that practically all CGIs are transcription start sites (TSS), largely of housekeeping and developmentally important genes [47, 48]. Approximately 70%

The relationship between structure and function is seen most vividly in many of the compo‐ sitional characteristics of CGIs. For instance, a recent study found that the CGI at the promoters of a particular group of genes was relatively nucleosome-deficient [50]. That is, the underlying DNA was highly accessible to activating transcription factors because less of it was spun around nucleosomes. Evidence from additional studies has shown that this nucleosome

be propagated in somatic cells are established [40].

As a result, the ideal situation would be an O/E of 1.

of all gene promoters are CGIs [49].

PHD domain [26].

6 Epigenetics and Epigenomics

*2.2.2. CpG Islands*

The long-standing study of DNA methylation took a significant turn in 2009 with the redis‐ covery of what is now commonly referred to as the "6th base pair:" 5-hydroxymethylcytosine (5hmC) [65]. This base is the product of an enzymatic reaction that adds a hydroxyl (-OH) group to the methyl of 5-methylcytosine as shown in Figure 2. 5hmC was initially detected in 1972 in mammalian DNA [66], but has since been found primarily, and abundantly, in Purkinje neurons [67], the central nervous system (in the brainstem, spinal cord, and especially the cerebellum [67] and cerebral cortex) [68], and in embryonic stem (ES) cells [65, 69]. The highest tissue levels of 5hmC have been consistently found in the brain [69-71]. The striking abundance of 5hmC in ES cells and PGCs has led scientists to delve into the possibility that 5hmC is linked with the removal of 5mC in such settings, *in vivo*. There is evidence to suggest that, unlike 5mC, 5hmC may be correlated with transcriptional activation, after having been found at euchromatic regions in mice [72, 73]. In essence, while 5mC is known to be a mark of tran‐ scriptional repression, 5hmC may be associated with turning genes back on. Since 2009, a large quantity of research has been generated, dedicated to studying the potential role of 5hmC in gene expression regulation. Despite this, we have only just scratched the surface of discovery as the role of 5hmC in the genome continues to remain highly elusive.

A vital question regarding 5hmC is whether it functions as an intermediate in enzymatic reactions or as a stable entity unto itself. In this chapter, considerable space will be dedicated to discussing the possible demethylation pathways in which 5hmC is speculated to be involved. In this and many contexts, demethylation is defined to be the removal of 5mC and

been shown to greatly inhibit the binding of these MBDs to DNA [80-82]. On the same note, DNMT1 is also well known to recruit H3K9 methyltransferases, but the enzyme is blocked by the very presence of 5hmC, so the likelihood of H3K9 methyltransferase binding is also reduced. Methylation has also been implicated in nucleosome compaction, making DNA less accessible to transcription factors [83]. Conversely, the effect of 5hmC on nucleosome com‐ paction has yet to be determined, but the nuclei of Purkinje neurons have been reported to

Epigenetic Mechanisms of the Vascular Endothelium

http://dx.doi.org/10.5772/58569

9

This figure is adapted from Matouk CC, Turgeon PJ, Marsden PA. Epigenetics and stroke risk-beyond the static DNA

**Figure 2.** Methyl modification to cytosine and hydroxyl addition to 5-methylcytosine. The addition of a methyl group at the 5-position of cytosine is mediated by the DNA methyltransferase (DNMT) family, where S-adenosylmethionine serves as the methyl donor. Notes: The ten-eleven translocation (TET) family of enzymes is able to oxidize 5-methylcy‐ tosine to 5-hydroxymethylcytosine in an oxygen-dependent reaction requiring adenosine triphosphate and 2-oxoglu‐ tarate. Cytosine can then be generated from the action of putative demethylases on 5-hydroxymethylcytosine, but has

The 2009 seminal paper by Tahiliani *et al.* identified the TET (ten-eleven translocation) enzymes as being those responsible for the generation of 5hmC by the hydroxylation of 5mC [65]. Adding yet another layer of complexity to uncovering the role of 5hmC in the genome, TET enzymes are also responsible for the further oxidation of 5hmC into new products: 5-formyl‐ cytosine (5fC) and 5-carboxycytosine (5caC) (70, 85, 86). TET enzymes are present throughout the Metazoa and the three forms, TET1, TET2, and TET3, are thought to have arisen as a result of a triplication event that occurred in jawed vertebrates [87]. All three murine forms have been seen to oxidize 5mC to 5hmC *in vitro* and *in vivo* [88, 89]. Moreover, the presence of 5mC consistently appears to be a pre-requisite for the generation of 5hmC *in vivo* [69, 72], suggesting that TET-mediated oxidation is the only means of formation. All of the TET proteins are Fe+2 and 2-oxoglutarate dependent dioxygenases (65, 88, 90). The term, *dioxygenase*, refers to an enzyme that catalyzes the addition of both oxygen atoms from molecular oxygen to another organic substrate. The iron ion is utilized as a co-factor, whereas 2-oxoglutarate is a co-

exhibit marked decondensation [84].

code. Advances in Genomics and Genetics. 2012;2012:2:67-84.

*2.2.4. Ten eleven-translocation (TET) enzymes*

not yet been fully described.

substrate.

CpG islands are regions of the genome that have remained CpG, rather than TpG rich, the latter being the product of CpG deamination that has taken place over evolutionary time. O/E indicates the ratio of observed CpG sites: expected number of CpG sites. Strong CGIs tend to have a high O/E meaning that the number of observed CpG sites is approaching the expected number of CpG sites, making for a maximum O/E of 1. Often unmethylated, these regions of the genome are associated with transcription start sites. A number of epigenetic patterns have been found to characterize CGIs (H3K36me2=dimethylation of lysine 36 on histone H3 and H3K4me3=trimethylation of lysine 4 on histone H3).

**Table 1.** Characteristics of CpG Islands (CGIs)

(eventual) replacement by cytosine. In the majority of these pathways where 5hmC is required, it is often thought to act as an intermediate, rapidly replaced by another chemical species. Levels of 5hmC are substantially lower than 5mC in the genome, at approximately 10% of 5mC and 0.4% of all cytosines [74]. These minute levels are thought to be consistent with the shortlived species hypothesis as elevated levels would indicate a longer duration. If 5hmC gener‐ ation is merely a pre-requisite for subsequent demethylation pathways regardless of what form they take, then 5hmC would be considered a transient species.

Evidence is also emerging which supports the notion of 5hmC as an entirely new landmark in the epigenetic gene regulatory landscape. In fact, the modified nitrogenous base may even be responsible for attracting a unique panel of chromatin and transcriptional modifiers. Numer‐ ous mechanisms have been proposed based on preliminary observations. Methyl-CpG binding domain protein 1 (MBD1) specifically recognizes methylated DNA and attracts histone deacetylases and H3 lysine 9 methyltransferases (also repressive in action) [75-79]. 5hmC has been shown to greatly inhibit the binding of these MBDs to DNA [80-82]. On the same note, DNMT1 is also well known to recruit H3K9 methyltransferases, but the enzyme is blocked by the very presence of 5hmC, so the likelihood of H3K9 methyltransferase binding is also reduced. Methylation has also been implicated in nucleosome compaction, making DNA less accessible to transcription factors [83]. Conversely, the effect of 5hmC on nucleosome com‐ paction has yet to be determined, but the nuclei of Purkinje neurons have been reported to exhibit marked decondensation [84].

This figure is adapted from Matouk CC, Turgeon PJ, Marsden PA. Epigenetics and stroke risk-beyond the static DNA code. Advances in Genomics and Genetics. 2012;2012:2:67-84.

**Figure 2.** Methyl modification to cytosine and hydroxyl addition to 5-methylcytosine. The addition of a methyl group at the 5-position of cytosine is mediated by the DNA methyltransferase (DNMT) family, where S-adenosylmethionine serves as the methyl donor. Notes: The ten-eleven translocation (TET) family of enzymes is able to oxidize 5-methylcy‐ tosine to 5-hydroxymethylcytosine in an oxygen-dependent reaction requiring adenosine triphosphate and 2-oxoglu‐ tarate. Cytosine can then be generated from the action of putative demethylases on 5-hydroxymethylcytosine, but has not yet been fully described.

#### *2.2.4. Ten eleven-translocation (TET) enzymes*

(eventual) replacement by cytosine. In the majority of these pathways where 5hmC is required, it is often thought to act as an intermediate, rapidly replaced by another chemical species. Levels of 5hmC are substantially lower than 5mC in the genome, at approximately 10% of 5mC and 0.4% of all cytosines [74]. These minute levels are thought to be consistent with the shortlived species hypothesis as elevated levels would indicate a longer duration. If 5hmC gener‐ ation is merely a pre-requisite for subsequent demethylation pathways regardless of what form

CpG islands are regions of the genome that have remained CpG, rather than TpG rich, the latter being the product of CpG deamination that has taken place over evolutionary time. O/E indicates the ratio of observed CpG sites: expected number of CpG sites. Strong CGIs tend to have a high O/E meaning that the number of observed CpG sites is approaching the expected number of CpG sites, making for a maximum O/E of 1. Often unmethylated, these regions of the genome are associated with transcription start sites. A number of epigenetic patterns have been found to characterize CGIs (H3K36me2=dimethylation of lysine 36 on histone H3 and H3K4me3=trimethylation of lysine 4 on histone H3).

Evidence is also emerging which supports the notion of 5hmC as an entirely new landmark in the epigenetic gene regulatory landscape. In fact, the modified nitrogenous base may even be responsible for attracting a unique panel of chromatin and transcriptional modifiers. Numer‐ ous mechanisms have been proposed based on preliminary observations. Methyl-CpG binding domain protein 1 (MBD1) specifically recognizes methylated DNA and attracts histone deacetylases and H3 lysine 9 methyltransferases (also repressive in action) [75-79]. 5hmC has

they take, then 5hmC would be considered a transient species.

**Table 1.** Characteristics of CpG Islands (CGIs)

8 Epigenetics and Epigenomics

The 2009 seminal paper by Tahiliani *et al.* identified the TET (ten-eleven translocation) enzymes as being those responsible for the generation of 5hmC by the hydroxylation of 5mC [65]. Adding yet another layer of complexity to uncovering the role of 5hmC in the genome, TET enzymes are also responsible for the further oxidation of 5hmC into new products: 5-formyl‐ cytosine (5fC) and 5-carboxycytosine (5caC) (70, 85, 86). TET enzymes are present throughout the Metazoa and the three forms, TET1, TET2, and TET3, are thought to have arisen as a result of a triplication event that occurred in jawed vertebrates [87]. All three murine forms have been seen to oxidize 5mC to 5hmC *in vitro* and *in vivo* [88, 89]. Moreover, the presence of 5mC consistently appears to be a pre-requisite for the generation of 5hmC *in vivo* [69, 72], suggesting that TET-mediated oxidation is the only means of formation. All of the TET proteins are Fe+2 and 2-oxoglutarate dependent dioxygenases (65, 88, 90). The term, *dioxygenase*, refers to an enzyme that catalyzes the addition of both oxygen atoms from molecular oxygen to another organic substrate. The iron ion is utilized as a co-factor, whereas 2-oxoglutarate is a cosubstrate.

The mammalian TET enzymes all exhibit a high degree of homology amongst their C terminal domains. It is the Cys-rich and double stranded-helix DSBH region (CD domain) [87] belong‐ ing to the Cupin-like dioxygenase superfamily, that contains the catalytic domain for 2 oxoglutarate and iron (II) activity [65, 88]. Further oxidation of 5hmC into 5fC and 5caC also takes place at this same active site [85]. This CD domain also contains the largest identifiable portion of the enzyme: the spacer region. For the most part, the function of this region is unknown, although some leads for future research do exist. For instance, Upabhyay *et al*. noted remarkable sequence overlap between the spacer region of TET1 and the C-terminal domain of RNA polymerase II of *S. cerevisiae*[91]. Likely of most significance are the conserved residues that are key sites for posttranslational modifications such as histone methylation and phos‐ phorylation [92]. Located on the N terminus (~60 amino acids) of TET1 and TET3 (not TET2) enzymes is the CXXC zinc finger domain [65, 87]. Even though its function has not been conclusively determined, the CXXC domain in TET1 has been shown to bind to unmodified cytosine, as well as 5mC and 5hmC [93, 94]. Speculation has tended towards this domain serving as the functional unit responsible for directing the enzymes to particular genomic regions, almost always CpG sites, so they can execute their oxidative action [92]. A similar CXXC domain on DNMT1, the enzyme on which it was first discovered, possesses comparable DNA binding properties [95], initially having suggested an equivalent role for the domain in TETs.

to the chromosome from which it was transcribed allows for allele specific recruitment of the

Epigenetic Mechanisms of the Vascular Endothelium

http://dx.doi.org/10.5772/58569

11

Another important lncRNA in X chromosome inactivation is the *Xist* antisense RNA, Tsix. Tsix is expressed on the active chromosome and blocks *Xist* expression, thereby preventing its inactivation [103]. The action of Tsix illustrates another mechanism of epigenetic regulation in which lncRNA can take part: DNA methylation. Recently, evidence has suggested that Tsix mediates DNA methylation at the *Xist* promoter, silencing the *Xist* gene [104]. Tsix may activate DNA methyltransferase 3A (DNMT3A), one of the *de novo* methyltransferases, and guide it to the *Xist* promoter where it is involved in maintaining the silencing of the *Xist* gene

X chromosome inactivation is not the only cellular process in which lncRNA is involved, and there are numerous other examples of lncRNAs as epigenetic regulators. For example, HOTAIR is an lncRNA located in the homeobox C (HOXC) cluster of genes [105]. The *HOX* genes are a family of genes that serve as developmental cues in the embryo [106]. The expres‐ sion pattern of different *HOX* genes corresponds to specific tissue development and ensures the correct relative positions of body parts. The 39 *HOX* genes are present in 4 gene clusters, HOXA-D, each present on a separate chromosome [107]. HOTAIR is expressed in the HOXC cluster where it acts in *trans* to suppress expression on the HOXD cluster. In this way, HOTAIR is required to maintain the specific expression pattern of *HOX* genes throughout embryonic development. Like the *Xist* RNA, HOTAIR achieves this repression through the recruitment of the PRC2 complex, which then catalyzes the repressive H3K27 trimethylation mark. Indeed, knockdown of HOTAIR has shown loss of H3K27 trimethylation in the HOXD gene cluster, as well as an absence of the PRC2 complex. This suggests that ncRNA may be a global

Most methylation patterns are stably inherited, remaining static throughout the lifetime of an organism. Specific cellular processes as well as cell-lineage specificity require activation or elimination of these patterns. Fluctuations in 5mC and 5hmC levels are most vividly seen in the cases of pre-implantation development and primordial germ cell formation (Figure 3). In order to understand the significance of the rapid changes in modified cytosine levels, a number

Throughout the duration of development, especially cellular differentiation, somatic-cell lineages acquire specialized DNA methylation and histone modification patterns. Even in the earliest stages, both sperm and oocyte are known to contain appreciable levels of DNA methylation. Many of the methylated regions are shared between oocyte and sperm, such as intracisternal A particles (IAPs) [108], although there are differentially methylated regions (DMRs) which is oocyte-or sperm-specific. Active and repressive histone modifications are

PRC2 complex and subsequent inactivation [101].

requirement for activation of PRC2 H3K27me3.

**3. DNA methylation and development**

**a. Pre-implantation embryo**

of recent and vital observations must be taken into account.

after initial repression.

#### **2.3. Long non-coding RNA**

Contrary to the central dogma of biology, in which RNA plays a passive role in transmitting genetic information to be translated into proteins, recent advances have shown RNA to play a much more active role in cellular regulation. Long non-coding RNAs (lncRNAs) are the most recent and least well characterized of functional "non-coding" RNAs. The distinction between lncRNAs and miRNAs is arbitrary, but has been defined as greater than 200 nucleotides for an lncRNA [96]. Unlike miRNAs, however, which seem to function through similar pathways, lncRNAs have been shown to play a diverse assortment of regulatory roles, including posttranscriptional repression, RNA splicing, and RNA degradation [97]. Despite this variety, perhaps the most interesting and well-studied mechanism is the ability of many lncRNAs to act as epigenetic modulators, interacting with chromatin remodeling complexes and other epigenetic machinery [98].

*Xist* was one of the first lncRNAs to be discovered [99] and, consequently, is the most well described. The *Xist* gene is found in the X chromosome inactivating center (XIC) where it plays a major role in the inactivation of one of the two X chromosomes in females [100], a process which equalizes X chromosome dosage to that of a male karyotype. *Xist* acts in *cis* to repress the transcription of the chromosome on which it is transcribed [101]. *Xist*'s function as an epigenetic regulator was confirmed with the discovery of an interacting factor, the polycomb repressive complex 2 (PRC2) [102], a complex that mediates the repressive histone trimethy‐ lation mark H3K27me3. PRC2 is recruited to the inactive X chromosome (*Xi*) by a short repetitive sequence, Repeat A (*RepA*), conserved on the *Xist* transcript [102]. Tethering of *Xist* to the chromosome from which it was transcribed allows for allele specific recruitment of the PRC2 complex and subsequent inactivation [101].

Another important lncRNA in X chromosome inactivation is the *Xist* antisense RNA, Tsix. Tsix is expressed on the active chromosome and blocks *Xist* expression, thereby preventing its inactivation [103]. The action of Tsix illustrates another mechanism of epigenetic regulation in which lncRNA can take part: DNA methylation. Recently, evidence has suggested that Tsix mediates DNA methylation at the *Xist* promoter, silencing the *Xist* gene [104]. Tsix may activate DNA methyltransferase 3A (DNMT3A), one of the *de novo* methyltransferases, and guide it to the *Xist* promoter where it is involved in maintaining the silencing of the *Xist* gene after initial repression.

X chromosome inactivation is not the only cellular process in which lncRNA is involved, and there are numerous other examples of lncRNAs as epigenetic regulators. For example, HOTAIR is an lncRNA located in the homeobox C (HOXC) cluster of genes [105]. The *HOX* genes are a family of genes that serve as developmental cues in the embryo [106]. The expres‐ sion pattern of different *HOX* genes corresponds to specific tissue development and ensures the correct relative positions of body parts. The 39 *HOX* genes are present in 4 gene clusters, HOXA-D, each present on a separate chromosome [107]. HOTAIR is expressed in the HOXC cluster where it acts in *trans* to suppress expression on the HOXD cluster. In this way, HOTAIR is required to maintain the specific expression pattern of *HOX* genes throughout embryonic development. Like the *Xist* RNA, HOTAIR achieves this repression through the recruitment of the PRC2 complex, which then catalyzes the repressive H3K27 trimethylation mark. Indeed, knockdown of HOTAIR has shown loss of H3K27 trimethylation in the HOXD gene cluster, as well as an absence of the PRC2 complex. This suggests that ncRNA may be a global requirement for activation of PRC2 H3K27me3.

## **3. DNA methylation and development**

Most methylation patterns are stably inherited, remaining static throughout the lifetime of an organism. Specific cellular processes as well as cell-lineage specificity require activation or elimination of these patterns. Fluctuations in 5mC and 5hmC levels are most vividly seen in the cases of pre-implantation development and primordial germ cell formation (Figure 3). In order to understand the significance of the rapid changes in modified cytosine levels, a number of recent and vital observations must be taken into account.

#### **a. Pre-implantation embryo**

The mammalian TET enzymes all exhibit a high degree of homology amongst their C terminal domains. It is the Cys-rich and double stranded-helix DSBH region (CD domain) [87] belong‐ ing to the Cupin-like dioxygenase superfamily, that contains the catalytic domain for 2 oxoglutarate and iron (II) activity [65, 88]. Further oxidation of 5hmC into 5fC and 5caC also takes place at this same active site [85]. This CD domain also contains the largest identifiable portion of the enzyme: the spacer region. For the most part, the function of this region is unknown, although some leads for future research do exist. For instance, Upabhyay *et al*. noted remarkable sequence overlap between the spacer region of TET1 and the C-terminal domain of RNA polymerase II of *S. cerevisiae*[91]. Likely of most significance are the conserved residues that are key sites for posttranslational modifications such as histone methylation and phos‐ phorylation [92]. Located on the N terminus (~60 amino acids) of TET1 and TET3 (not TET2) enzymes is the CXXC zinc finger domain [65, 87]. Even though its function has not been conclusively determined, the CXXC domain in TET1 has been shown to bind to unmodified cytosine, as well as 5mC and 5hmC [93, 94]. Speculation has tended towards this domain serving as the functional unit responsible for directing the enzymes to particular genomic regions, almost always CpG sites, so they can execute their oxidative action [92]. A similar CXXC domain on DNMT1, the enzyme on which it was first discovered, possesses comparable DNA binding properties [95], initially having suggested an equivalent role for the domain in

Contrary to the central dogma of biology, in which RNA plays a passive role in transmitting genetic information to be translated into proteins, recent advances have shown RNA to play a much more active role in cellular regulation. Long non-coding RNAs (lncRNAs) are the most recent and least well characterized of functional "non-coding" RNAs. The distinction between lncRNAs and miRNAs is arbitrary, but has been defined as greater than 200 nucleotides for an lncRNA [96]. Unlike miRNAs, however, which seem to function through similar pathways, lncRNAs have been shown to play a diverse assortment of regulatory roles, including posttranscriptional repression, RNA splicing, and RNA degradation [97]. Despite this variety, perhaps the most interesting and well-studied mechanism is the ability of many lncRNAs to act as epigenetic modulators, interacting with chromatin remodeling complexes and other

*Xist* was one of the first lncRNAs to be discovered [99] and, consequently, is the most well described. The *Xist* gene is found in the X chromosome inactivating center (XIC) where it plays a major role in the inactivation of one of the two X chromosomes in females [100], a process which equalizes X chromosome dosage to that of a male karyotype. *Xist* acts in *cis* to repress the transcription of the chromosome on which it is transcribed [101]. *Xist*'s function as an epigenetic regulator was confirmed with the discovery of an interacting factor, the polycomb repressive complex 2 (PRC2) [102], a complex that mediates the repressive histone trimethy‐ lation mark H3K27me3. PRC2 is recruited to the inactive X chromosome (*Xi*) by a short repetitive sequence, Repeat A (*RepA*), conserved on the *Xist* transcript [102]. Tethering of *Xist*

TETs.

**2.3. Long non-coding RNA**

10 Epigenetics and Epigenomics

epigenetic machinery [98].

Throughout the duration of development, especially cellular differentiation, somatic-cell lineages acquire specialized DNA methylation and histone modification patterns. Even in the earliest stages, both sperm and oocyte are known to contain appreciable levels of DNA methylation. Many of the methylated regions are shared between oocyte and sperm, such as intracisternal A particles (IAPs) [108], although there are differentially methylated regions (DMRs) which is oocyte-or sperm-specific. Active and repressive histone modifications are present in the oocyte at this time [109], and it is maternally inherited proteins that will direct the events of early cleavage divisions. On the other hand, sperm arrive with temporary histone substitutes, protamines, which play a similarly functional role in packaging [110].

instilled (Figure 3). That is, no more demethylation is known to take place because patterns placed onto the genome at this stage are the same as those that will be found in somatic cells of later development and maturation. This *de novo* methylation is now known to be catalyzed by the *de novo* methyltransferases 3A and 3B [116]. In fact, inactivation of both DNMT3A and 3B has been shown to result in early embryonic lethality while mutations in the encoding genes have also resulted in postnatal or embryonic lethality [126, 127]. Establishing the patterns of the genome at this stage allows for the predictable mitotic transmission of methylation marks

Epigenetic Mechanisms of the Vascular Endothelium

http://dx.doi.org/10.5772/58569

13

As opposed to the undoubtedly critical role of TET3 following fertilization in mice, TET1 and TET2 are thought to have modulatory, yet not essential roles in development, ES cell endur‐ ance, and pluripotency [84]. At the blastula stage, the function of TET1 and TET2 proteins in the inner cell mass is likely to repress lineage-specific genes, counteracting the effect of methylation, so as to permit activation of certain genes later in development [128, 129]. Consequently, they are thought to be fine tuning methylation patterns at this point [84].

Consistent experimental results indicate that there is, however, much still to be confirmed about the relative role of TET proteins in development. As a point of discrepancy, TET1 deficient mouse ES cells have been seen to maintain their self-renewal capabilities *in vitro* and develop ordinarily *in vivo* [130]. Furthermore, numerous groups have demonstrated that the knockout of both TET1 and TET2 results in the normal development and healthy adulthood of fertile mice [130-134]. It is hypothesized that such discrepancies may be a result of the alternate TET proteins compensating for the depletion of one another [92]. Although the biological roles of TET1 and TET2 in zygotic development are still highly disputable, that of TET3 appears to be more comprehensive. One study, in particular, highlighted the importance of this particular enzyme in embryogenesis by introducing a homozygous mutation in the TET3 encoding gene, subsequently observing neonatal lethality [119]. The same study came to the conclusion that failure to demethylate the male pronucleus is a direct result of TET3

Evidently, epigenetic modifications play an unquestionably enormous role in early develop‐ ment. Despite remaining relatively constant in the mitotic transmission of later development, methylation patterns undergo rapid, yet precisely timed fluctuations in zygotic development. 5hmC abundance points to a vital role of the TET enzymes, as no other pathway has been conclusively verified for the generation of hydroxymethylcytosine from methylcytosine. In light of the recent re-discovery of 5hmC and already substantial amount of scientific inquiry that has gone into deciphering its role in development, we can hope for a great deal more to

Primordial germ cells (PGCs) are the cells that ultimately give rise to the germ line, the oocyte and sperm. Similar to what has been observed in zygotic development, mouse PGCs, derived from epiblast cells, are known to experience a correspondingly fast decline in 5mC levels [135] between embryonic day (E) 9.5 and 13.5 [124, 136, 137]. Very recently, Hackett *et al.* decisively demonstrated that the demethylation that takes place in PGCs is conceptually equivalent to

throughout the lifetime of an organism [40].

depletion.

come in the near future!

**b. Primordial Germ Cells**

Upon fertilization, the sperm genome is the earliest to undergo major modifications, the first of which is protamine removal and substitution with histones [111]. Prior to the fusion of the maternal and paternal pronuclei, a vast genome-wide demethylation event occurs in the paternal pronucleus [112-115], whereby its methylation patterns are erased almost in their entirety. This event can occur in as few as six hours following fertilization [112, 113, 116]. This demethylation has been assessed repeatedly via immunostaining with antibodies specific for 5mC [112, 113, 116] as well as bisulfite sequencing which has clearly shown that one of two genomes becomes demethylated. A recently discovered and intriguing fact is that this genomewide demethylation is actually a mass oxidation event [117-119]. 5mC specific antibodies do not recognize 5hmC or any other oxidized cytosine, yet it has been repeatedly and conclusively demonstrated that the male pronucleus does exhibit a marked increase in 5hmC levels at this time [117-119]. Complimentary antibody staining has taken place in order to deduce this. Regions unaffected by this event include paternal DMRs in imprinted genes [120, 121] and IAPs [108]. It is now well known that it is the maternal TET3 enzyme that executes the oxidative action on the paternal pronucleus [119]. In contrast to the other TET enzymes, TET3 knock‐ down has been demonstrated to result in the near deficit of 5hmC.

The presence of histone modifications unique to the maternal pronucleus is linked to its spared erasure at this time of otherwise mass oxidation. Developmental pluripotency-associated 3 protein (DPPA3, also known as stella), has been identified as the key protector of the maternal pronucleus as well as that of a few paternally imprinted genes [122]. As a matter of fact, the protection offered by this protein is almost indisputable, as experiments have shown that an absence of DPPA3 results in the hydroxymethylation of both paternal and maternal genomes [117, 122]. This protein was originally identified as a result of the upregulation of its encoding gene during initial PGC development [123]. Dimethylation of H3 histone at lysine 9, a mark that is restricted to these sites [122], has been reported to be responsible for the attraction of DPPA3 to these regions.

As indicated in Figure 3, the 2-16 cell stage exhibits a substantial decrease in both maternal‐ ly dominant 5mC and paternally specific 5hmC levels. It is a well known fact that the maternal genome also loses all methylation marks during early embryogenesis. This, however, has not been attributed to a mass oxidation event, hence, no generation of 5hmC takes place at this time. The cytoplasmic localization of DNMT1o, a splice variant of DNMT1, is attributed to the passive replication-dependent dilution of all oxidized cyto‐ sines, [112, 116, 124] accounting also for maternal genome methylation erasure. That is, with each division, 50% of the genomic methylation and hydroxymethylation patterns are lost due to the absence of maintenance methylation [125], until virtually no modified cyto‐ sines remain by the sixteen cell stage [112, 116].

Another generally accepted fact is that a wave of *de novo* methylation takes place at approxi‐ mately the time when the blastula implants into the uterus [116, 120]. This activity occurs very rapidly and 5mC levels plateau once all of the necessary methylation patterns have been instilled (Figure 3). That is, no more demethylation is known to take place because patterns placed onto the genome at this stage are the same as those that will be found in somatic cells of later development and maturation. This *de novo* methylation is now known to be catalyzed by the *de novo* methyltransferases 3A and 3B [116]. In fact, inactivation of both DNMT3A and 3B has been shown to result in early embryonic lethality while mutations in the encoding genes have also resulted in postnatal or embryonic lethality [126, 127]. Establishing the patterns of the genome at this stage allows for the predictable mitotic transmission of methylation marks throughout the lifetime of an organism [40].

As opposed to the undoubtedly critical role of TET3 following fertilization in mice, TET1 and TET2 are thought to have modulatory, yet not essential roles in development, ES cell endur‐ ance, and pluripotency [84]. At the blastula stage, the function of TET1 and TET2 proteins in the inner cell mass is likely to repress lineage-specific genes, counteracting the effect of methylation, so as to permit activation of certain genes later in development [128, 129]. Consequently, they are thought to be fine tuning methylation patterns at this point [84].

Consistent experimental results indicate that there is, however, much still to be confirmed about the relative role of TET proteins in development. As a point of discrepancy, TET1 deficient mouse ES cells have been seen to maintain their self-renewal capabilities *in vitro* and develop ordinarily *in vivo* [130]. Furthermore, numerous groups have demonstrated that the knockout of both TET1 and TET2 results in the normal development and healthy adulthood of fertile mice [130-134]. It is hypothesized that such discrepancies may be a result of the alternate TET proteins compensating for the depletion of one another [92]. Although the biological roles of TET1 and TET2 in zygotic development are still highly disputable, that of TET3 appears to be more comprehensive. One study, in particular, highlighted the importance of this particular enzyme in embryogenesis by introducing a homozygous mutation in the TET3 encoding gene, subsequently observing neonatal lethality [119]. The same study came to the conclusion that failure to demethylate the male pronucleus is a direct result of TET3 depletion.

Evidently, epigenetic modifications play an unquestionably enormous role in early develop‐ ment. Despite remaining relatively constant in the mitotic transmission of later development, methylation patterns undergo rapid, yet precisely timed fluctuations in zygotic development. 5hmC abundance points to a vital role of the TET enzymes, as no other pathway has been conclusively verified for the generation of hydroxymethylcytosine from methylcytosine. In light of the recent re-discovery of 5hmC and already substantial amount of scientific inquiry that has gone into deciphering its role in development, we can hope for a great deal more to come in the near future!

### **b. Primordial Germ Cells**

present in the oocyte at this time [109], and it is maternally inherited proteins that will direct the events of early cleavage divisions. On the other hand, sperm arrive with temporary histone

Upon fertilization, the sperm genome is the earliest to undergo major modifications, the first of which is protamine removal and substitution with histones [111]. Prior to the fusion of the maternal and paternal pronuclei, a vast genome-wide demethylation event occurs in the paternal pronucleus [112-115], whereby its methylation patterns are erased almost in their entirety. This event can occur in as few as six hours following fertilization [112, 113, 116]. This demethylation has been assessed repeatedly via immunostaining with antibodies specific for 5mC [112, 113, 116] as well as bisulfite sequencing which has clearly shown that one of two genomes becomes demethylated. A recently discovered and intriguing fact is that this genomewide demethylation is actually a mass oxidation event [117-119]. 5mC specific antibodies do not recognize 5hmC or any other oxidized cytosine, yet it has been repeatedly and conclusively demonstrated that the male pronucleus does exhibit a marked increase in 5hmC levels at this time [117-119]. Complimentary antibody staining has taken place in order to deduce this. Regions unaffected by this event include paternal DMRs in imprinted genes [120, 121] and IAPs [108]. It is now well known that it is the maternal TET3 enzyme that executes the oxidative action on the paternal pronucleus [119]. In contrast to the other TET enzymes, TET3 knock‐

The presence of histone modifications unique to the maternal pronucleus is linked to its spared erasure at this time of otherwise mass oxidation. Developmental pluripotency-associated 3 protein (DPPA3, also known as stella), has been identified as the key protector of the maternal pronucleus as well as that of a few paternally imprinted genes [122]. As a matter of fact, the protection offered by this protein is almost indisputable, as experiments have shown that an absence of DPPA3 results in the hydroxymethylation of both paternal and maternal genomes [117, 122]. This protein was originally identified as a result of the upregulation of its encoding gene during initial PGC development [123]. Dimethylation of H3 histone at lysine 9, a mark that is restricted to these sites [122], has been reported to be responsible for the attraction of

As indicated in Figure 3, the 2-16 cell stage exhibits a substantial decrease in both maternal‐ ly dominant 5mC and paternally specific 5hmC levels. It is a well known fact that the maternal genome also loses all methylation marks during early embryogenesis. This, however, has not been attributed to a mass oxidation event, hence, no generation of 5hmC takes place at this time. The cytoplasmic localization of DNMT1o, a splice variant of DNMT1, is attributed to the passive replication-dependent dilution of all oxidized cyto‐ sines, [112, 116, 124] accounting also for maternal genome methylation erasure. That is, with each division, 50% of the genomic methylation and hydroxymethylation patterns are lost due to the absence of maintenance methylation [125], until virtually no modified cyto‐

Another generally accepted fact is that a wave of *de novo* methylation takes place at approxi‐ mately the time when the blastula implants into the uterus [116, 120]. This activity occurs very rapidly and 5mC levels plateau once all of the necessary methylation patterns have been

substitutes, protamines, which play a similarly functional role in packaging [110].

down has been demonstrated to result in the near deficit of 5hmC.

DPPA3 to these regions.

12 Epigenetics and Epigenomics

sines remain by the sixteen cell stage [112, 116].

Primordial germ cells (PGCs) are the cells that ultimately give rise to the germ line, the oocyte and sperm. Similar to what has been observed in zygotic development, mouse PGCs, derived from epiblast cells, are known to experience a correspondingly fast decline in 5mC levels [135] between embryonic day (E) 9.5 and 13.5 [124, 136, 137]. Very recently, Hackett *et al.* decisively demonstrated that the demethylation that takes place in PGCs is conceptually equivalent to

erasure so as to ensure that gender-specific methylation associated with imprinting can be put into place during the remainder of germ cell development [123]. Demethylation at this time has also been proposed to be responsible for reinstating the pluripotent state in PGCs. Clearly, those regions whose expression had been repressed are now turned on, allowing for the germ cell lineage acquisition of pluripotent characteristics, perhaps a pre-requisite to achievement of totipotency. Similar to the spared erasure of paternally imprinted genes in zygotic devel‐ opment, certain transposons such as IAPs remain moderately methylated at this time [34].

Epigenetic Mechanisms of the Vascular Endothelium

http://dx.doi.org/10.5772/58569

15

In contrast to zygotic development, the demethylation of imprinted regions is absolutely critical because germ cells possess imprints that are uniquely exclusive to the gender of the organism. As indicated in the bottom half of Figure 3, an analogous round of *de novo* methyl‐ ation also takes place later in oogenesis and spermatogenesis. Re-methylation along with the re-installation of imprints starts at approximately E15 in males and, in females, after birth [139].

As illustrated above, it is a well ingrained fact that epigenetic reprogramming does take place in zygotic development and PGC formation. More recently, TET protein activity has been observed in relation to the timing of particular developmental events. Consequently, levels of 5hmC have been monitored and correlated with the activity of TET proteins at each stage of interest. Truly novel is the fact that this reprogramming involves a mass oxidation event, that is, the generation of 5hmC. The function of 5hmC in these stages is a highly debated and controversial area of research. We have already addressed the first disputed issue regarding the stability of this oxidized base, but we will now draw our attention to the second debate: What are the possible demethylation pathways by which reprogramming takes place? We will define demethylation as the eventual replacement of 5mC with unmodified cytosine. Possible mechanisms for this can be broadly grouped into passive and active pathways. In analyzing the possibilities, it is important to note that absolutely no consensus exists as to which mechanism predominates and that there is experimental evidence to both confirm and rebuke

Passive demethylation is fairly well established as one of perhaps several operating processes. As mentioned above, the maintenance DNMT places methylation patterns on a progeny strand using the parental strand as a template, similar to the synthesis of a new strand of DNA whereby DNA polymerase utilizes the parent strand as a template for construction of a complementarily base-paired DNA strand. Like the DNA double helix, the maintenance of methylation patterns also occurs through a semi-conservative pathway. This particular setup yields a hemi-methylated (partly methylated) pattern on the DNA. UHRF1 binding and PCNA recruitment are the first steps in the faithful copying of methylation patterns from one strand to another, thereby ensuring the transmission of methylation patterns through mitotic division. From the perspective of demethylation pathways, if this faithful re-installation of methylation patterns is disturbed, every generation will subsequently exhibit 50% less methylation. Eventually, such patterns will undergo what is called passive replication-dependent dilution.

**3.1. DNA demethylation pathways**

nearly all pathways.

*3.1.1. Passive demethylation*

**Figure 3.** Dynamic nature of 5mC, 5hmC, and TET enzyme levels in the pre-implantation embryo and primordial germ cell development. Intensity of purple shading indicates the relative level of modified cytosine at that stage in develop‐ ment. Green shading indicates high levels of TET3 activity, while blue shading shows elevated levels of TET1 and TET2 at these stages in development. Sperm and oocyte begin with high levels of 5mC. Paternal methylation patterns are erased just after fertilization and a mass oxidation event takes place with increasing levels of 5hmC by the zygotic stage. 5mC and 5hmC (from the paternal genome) levels diminish by means of a passive-replication dependent man‐ ner whereby both the maternal and paternal genomes are practically devoid of either modified cytosine by the 16 cell stage. Upon implantation in the uterus, mass *denovo* methylation takes place whereby somatic cell methylation pat‐ terns are established. Primordial germ cells are also subject to demethylation between E9.5 and E13.5, accompanied by increasing 5hmC levels until approximately E 11. Paternal re-methylation takes place beginning at about E15 and, in females, after birth.

the mass oxidation event that has been observed during embryonic development. In this case, TET1 and TET2 are responsible for the generation of 5hmC [124, 138].

Thus far, the acquisition of 5hmC appears to take place between E9.5 and E11.5 [124], but seems to be lost at a rate that is typical of replication-dependent pattern dilution [124]. Such circum‐ stances closely parallel those seen in zygotic development. In the same way that the DNMT1o splice variant has been seen to be excluded from the nucleus in zygotic development, UHRF1 consistently appears to be down-regulated in PGC formation [84]. Such a situation prevents DNMT1 from performing its prescribed action. Evidence indicates that TET-mediated oxidation in PGCs is likely made possible by passive, rather than active demethylation [124]. This observation is further substantiated by the absence of both 5fC and 5caC following PGC demethylation, as shown in immunocytochemistry studies [124], whereas their presence in zygotic development indicates an increased likelihood for an active demethylation mechanism at work.

By definition, methylation patterns at CpG islands will never be erased during normal development. Yet, CpG island methylation in the DMR of imprinted genes must undergo erasure so as to ensure that gender-specific methylation associated with imprinting can be put into place during the remainder of germ cell development [123]. Demethylation at this time has also been proposed to be responsible for reinstating the pluripotent state in PGCs. Clearly, those regions whose expression had been repressed are now turned on, allowing for the germ cell lineage acquisition of pluripotent characteristics, perhaps a pre-requisite to achievement of totipotency. Similar to the spared erasure of paternally imprinted genes in zygotic devel‐ opment, certain transposons such as IAPs remain moderately methylated at this time [34].

In contrast to zygotic development, the demethylation of imprinted regions is absolutely critical because germ cells possess imprints that are uniquely exclusive to the gender of the organism. As indicated in the bottom half of Figure 3, an analogous round of *de novo* methyl‐ ation also takes place later in oogenesis and spermatogenesis. Re-methylation along with the re-installation of imprints starts at approximately E15 in males and, in females, after birth [139].

### **3.1. DNA demethylation pathways**

As illustrated above, it is a well ingrained fact that epigenetic reprogramming does take place in zygotic development and PGC formation. More recently, TET protein activity has been observed in relation to the timing of particular developmental events. Consequently, levels of 5hmC have been monitored and correlated with the activity of TET proteins at each stage of interest. Truly novel is the fact that this reprogramming involves a mass oxidation event, that is, the generation of 5hmC. The function of 5hmC in these stages is a highly debated and controversial area of research. We have already addressed the first disputed issue regarding the stability of this oxidized base, but we will now draw our attention to the second debate: What are the possible demethylation pathways by which reprogramming takes place? We will define demethylation as the eventual replacement of 5mC with unmodified cytosine. Possible mechanisms for this can be broadly grouped into passive and active pathways. In analyzing the possibilities, it is important to note that absolutely no consensus exists as to which mechanism predominates and that there is experimental evidence to both confirm and rebuke nearly all pathways.

#### *3.1.1. Passive demethylation*

the mass oxidation event that has been observed during embryonic development. In this case,

**Figure 3.** Dynamic nature of 5mC, 5hmC, and TET enzyme levels in the pre-implantation embryo and primordial germ cell development. Intensity of purple shading indicates the relative level of modified cytosine at that stage in develop‐ ment. Green shading indicates high levels of TET3 activity, while blue shading shows elevated levels of TET1 and TET2 at these stages in development. Sperm and oocyte begin with high levels of 5mC. Paternal methylation patterns are erased just after fertilization and a mass oxidation event takes place with increasing levels of 5hmC by the zygotic stage. 5mC and 5hmC (from the paternal genome) levels diminish by means of a passive-replication dependent man‐ ner whereby both the maternal and paternal genomes are practically devoid of either modified cytosine by the 16 cell stage. Upon implantation in the uterus, mass *denovo* methylation takes place whereby somatic cell methylation pat‐ terns are established. Primordial germ cells are also subject to demethylation between E9.5 and E13.5, accompanied by increasing 5hmC levels until approximately E 11. Paternal re-methylation takes place beginning at about E15 and,

Thus far, the acquisition of 5hmC appears to take place between E9.5 and E11.5 [124], but seems to be lost at a rate that is typical of replication-dependent pattern dilution [124]. Such circum‐ stances closely parallel those seen in zygotic development. In the same way that the DNMT1o splice variant has been seen to be excluded from the nucleus in zygotic development, UHRF1 consistently appears to be down-regulated in PGC formation [84]. Such a situation prevents DNMT1 from performing its prescribed action. Evidence indicates that TET-mediated oxidation in PGCs is likely made possible by passive, rather than active demethylation [124]. This observation is further substantiated by the absence of both 5fC and 5caC following PGC demethylation, as shown in immunocytochemistry studies [124], whereas their presence in zygotic development indicates an increased likelihood for an active demethylation mechanism

By definition, methylation patterns at CpG islands will never be erased during normal development. Yet, CpG island methylation in the DMR of imprinted genes must undergo

TET1 and TET2 are responsible for the generation of 5hmC [124, 138].

at work.

in females, after birth.

14 Epigenetics and Epigenomics

Passive demethylation is fairly well established as one of perhaps several operating processes. As mentioned above, the maintenance DNMT places methylation patterns on a progeny strand using the parental strand as a template, similar to the synthesis of a new strand of DNA whereby DNA polymerase utilizes the parent strand as a template for construction of a complementarily base-paired DNA strand. Like the DNA double helix, the maintenance of methylation patterns also occurs through a semi-conservative pathway. This particular setup yields a hemi-methylated (partly methylated) pattern on the DNA. UHRF1 binding and PCNA recruitment are the first steps in the faithful copying of methylation patterns from one strand to another, thereby ensuring the transmission of methylation patterns through mitotic division. From the perspective of demethylation pathways, if this faithful re-installation of methylation patterns is disturbed, every generation will subsequently exhibit 50% less methylation. Eventually, such patterns will undergo what is called passive replication-dependent dilution. As mentioned, this appears to be the way in which the methylation patterns of the zygotic maternal genome are erased. Thus, the plausibility of this mechanism is not debated. Paternal genome erasure prior to replication is significant evidence that defies the notion of passive demethylation as the *only* demethylation pathway.

deformylation pathway involved in the direct conversion of 5fC to cytosine has also been

Epigenetic Mechanisms of the Vascular Endothelium

http://dx.doi.org/10.5772/58569

17

What about a simple removal of the 5mC base followed by TDG action? Scientists have noted that, due to the strength of the carbon-carbon bond needed to be broken, an enzyme with unwieldy catalytic power would be needed to achieve such a feat [140]. Methyl-CpG binding domain protein 2 (MBD2) was first and foremost reported to catalyze just such a reaction. By its very nature, MBD2 is known to *bind* to methylated cytosine, so it was often questioned how it could be responsible for mediating such an active reaction if it first must attach itself [28, 75]. Numerous other downfalls of this theory emerged and no lab was apparently able to replicate the results, so the theory of MBD2-mediated direct removal of the methyl group of 5mC fell out of favour. Hence, the inevitability of some sort of TDG/BER activity is further

A model plant used in genetics and epigenetics studies, *Arabidopsis thaliana*, is the only source that has thus far provided evidence for such a direct removal of 5mC (reviewed in [150]). The existence of ROS1, DME, DML2, and DML7-a family of four 5mC DNA glycosylases has been acknowledged in this plant [150]. Their preference for acting on 5mC in double stranded DNA, has led researchers to claim that these enzymes are indeed necessary for active demethylation of particular genes. The function of these glycosylases is similar to that of BER, in that a nick created leaves an abasic site which is rapidly repaired. Yet, the enzymes and mechanisms in mammals appear to be quite distinct from those that have been identified in the plant [151].

The second well investigated, yet still highly debated active replication-independent deme‐ thylation pathway is one which also utilizes a DNA repair pathway. AID (activation-induced cytidine deaminase) and APOBEC (apolipoprotein B mRNA editing enzymes, catalytic polypeptide) family members are primarily known for their ability to deaminate cytosine to uracil [152]. *In vitro* studies have demonstrated the further ability of AID/APOBEC to deami‐ nate 5mC in DNA, to thymine, resulting in a T:G mismatch [149]. The excision conducted by a TDG glycosylase would subsequently result in an abasic site (apurinic and apyrimidinic [AP] site) which would then be subject to repair by BER. The final product of such a chain reaction

There are a number of variations and caveats of this and related processes. For instance, AID and APOBEC have frequently been seen to function in a single-stranded DNA environment [149]. Deamination in single-stranded DNA has been experimentally observed *in vitro* and in an *E. coli* assay [149]. Despite this, AID and APOBEC are both present at appreciable levels in oocytes as well as PGCs, so their potential role in developmental demethylation has not been

An alternate pathway through which AID/APOBEC are thought to function involves the deamination of 5hmC to 5-hydroxymethyluracil (5hmU) and its subsequent removal by a TDG

would be the regeneration of cytosine in place of the modified base [149].

postulated.

substantiated [149].

*3.1.4. AID/APOBEC activity*

dismissed [149].

*3.1.3. Direct removal of 5-methylcytosine*

As far as active or replication-independent pathways go, the central tenets of a variety of these pathways will be discussed in the following. A common thread that runs beneath a number of these is the coupling of TET protein activity with a well known DNA repair pathway, base excision repair (BER), whereby a nitrogenous base is excised by a glycosylase enzyme and replaced with a new one. Some sort of replacement mechanism is practically inevitable given that an unmodified cytosine must take the place of a previous base in order to complete demethylation.

## *3.1.2. Pathways in which 5fC and 5caC are involved*

The first of these proposed pathways involves the other two oxidized bases, 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) that can be generated by further oxidation of 5hmC by TET enzymes [70, 85, 86]. Their presence at very low quantities in the genome (5fC: 0.03% of 5mC in mouse ES cells; 5caC: 0.01% of 5mC in mouse ES cells) [70, 85, 86], has been attributed to the preference of TET enzymes towards 5mC, not 5hmC, as a substrate, as well as an exceedingly fast removal of the oxidized bases [85, 140]. Thymine DNA glycosylases (TDGs) are capable of excising both bases once they are produced. Kinetic studies by Maiti & Drohat clearly demonstrated that TDG excises 5fC and 5caC, but not 5hmC [141]. Neither when left for a longer time nor performed at a lower temperature (for enzyme stability maintenance) was there any significant 5hmC excision [141]. Excision of the oxidized bases opens the door for base excision repair (BER) action that completes the guanine base on the opposite strand with a brand new cytosine, hence, completing the demethylation pathway. Several labs have confirmed that the proposed is a highly plausible mechanism [85, 141, 142].

Interestingly, a number of studies have shown that TDG exhibits strong specificity in its action: it excises bases which are complementarily base paired with G and/or those which are also followed by guanine [143-146]. Such an observation is entirely consistent with the proposed role of TDG and CpG sites [147] whereby the cytosine has undergone a further modification, yet still fulfills the remainder of the criteria. More research must be undertaken to confirm whether TDG action on modified cytosines, followed by BER, is a plausible demethylation mechanism *in vivo*. Whether such a pathway is of sufficient speed to play a role in demethy‐ lation is one concern which must be addressed. Another comes about when we consider the exceedingly minute quantities of both of the bases in the genome: How prevalent can this pathway realistically be? Is it enough to account for mass demethylation in both zygotic and PGC development?

There is limited evidence that supports a decarboxylation pathway of 5caC, mediated by proteins present in lysates of ES cells [148]. Although the factors that catalyze this reaction have yet to be concisely identified, Schiesser *et al.* utilized isotope tracing to detect the direct conversion of 5caC to cytosine without interference from BER [148]. The existence of a deformylation pathway involved in the direct conversion of 5fC to cytosine has also been postulated.

### *3.1.3. Direct removal of 5-methylcytosine*

As mentioned, this appears to be the way in which the methylation patterns of the zygotic maternal genome are erased. Thus, the plausibility of this mechanism is not debated. Paternal genome erasure prior to replication is significant evidence that defies the notion of passive

As far as active or replication-independent pathways go, the central tenets of a variety of these pathways will be discussed in the following. A common thread that runs beneath a number of these is the coupling of TET protein activity with a well known DNA repair pathway, base excision repair (BER), whereby a nitrogenous base is excised by a glycosylase enzyme and replaced with a new one. Some sort of replacement mechanism is practically inevitable given that an unmodified cytosine must take the place of a previous base in order to complete

The first of these proposed pathways involves the other two oxidized bases, 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) that can be generated by further oxidation of 5hmC by TET enzymes [70, 85, 86]. Their presence at very low quantities in the genome (5fC: 0.03% of 5mC in mouse ES cells; 5caC: 0.01% of 5mC in mouse ES cells) [70, 85, 86], has been attributed to the preference of TET enzymes towards 5mC, not 5hmC, as a substrate, as well as an exceedingly fast removal of the oxidized bases [85, 140]. Thymine DNA glycosylases (TDGs) are capable of excising both bases once they are produced. Kinetic studies by Maiti & Drohat clearly demonstrated that TDG excises 5fC and 5caC, but not 5hmC [141]. Neither when left for a longer time nor performed at a lower temperature (for enzyme stability maintenance) was there any significant 5hmC excision [141]. Excision of the oxidized bases opens the door for base excision repair (BER) action that completes the guanine base on the opposite strand with a brand new cytosine, hence, completing the demethylation pathway. Several labs have

Interestingly, a number of studies have shown that TDG exhibits strong specificity in its action: it excises bases which are complementarily base paired with G and/or those which are also followed by guanine [143-146]. Such an observation is entirely consistent with the proposed role of TDG and CpG sites [147] whereby the cytosine has undergone a further modification, yet still fulfills the remainder of the criteria. More research must be undertaken to confirm whether TDG action on modified cytosines, followed by BER, is a plausible demethylation mechanism *in vivo*. Whether such a pathway is of sufficient speed to play a role in demethy‐ lation is one concern which must be addressed. Another comes about when we consider the exceedingly minute quantities of both of the bases in the genome: How prevalent can this pathway realistically be? Is it enough to account for mass demethylation in both zygotic and

There is limited evidence that supports a decarboxylation pathway of 5caC, mediated by proteins present in lysates of ES cells [148]. Although the factors that catalyze this reaction have yet to be concisely identified, Schiesser *et al.* utilized isotope tracing to detect the direct conversion of 5caC to cytosine without interference from BER [148]. The existence of a

confirmed that the proposed is a highly plausible mechanism [85, 141, 142].

demethylation as the *only* demethylation pathway.

*3.1.2. Pathways in which 5fC and 5caC are involved*

demethylation.

16 Epigenetics and Epigenomics

PGC development?

What about a simple removal of the 5mC base followed by TDG action? Scientists have noted that, due to the strength of the carbon-carbon bond needed to be broken, an enzyme with unwieldy catalytic power would be needed to achieve such a feat [140]. Methyl-CpG binding domain protein 2 (MBD2) was first and foremost reported to catalyze just such a reaction. By its very nature, MBD2 is known to *bind* to methylated cytosine, so it was often questioned how it could be responsible for mediating such an active reaction if it first must attach itself [28, 75]. Numerous other downfalls of this theory emerged and no lab was apparently able to replicate the results, so the theory of MBD2-mediated direct removal of the methyl group of 5mC fell out of favour. Hence, the inevitability of some sort of TDG/BER activity is further substantiated [149].

A model plant used in genetics and epigenetics studies, *Arabidopsis thaliana*, is the only source that has thus far provided evidence for such a direct removal of 5mC (reviewed in [150]). The existence of ROS1, DME, DML2, and DML7-a family of four 5mC DNA glycosylases has been acknowledged in this plant [150]. Their preference for acting on 5mC in double stranded DNA, has led researchers to claim that these enzymes are indeed necessary for active demethylation of particular genes. The function of these glycosylases is similar to that of BER, in that a nick created leaves an abasic site which is rapidly repaired. Yet, the enzymes and mechanisms in mammals appear to be quite distinct from those that have been identified in the plant [151].

### *3.1.4. AID/APOBEC activity*

The second well investigated, yet still highly debated active replication-independent deme‐ thylation pathway is one which also utilizes a DNA repair pathway. AID (activation-induced cytidine deaminase) and APOBEC (apolipoprotein B mRNA editing enzymes, catalytic polypeptide) family members are primarily known for their ability to deaminate cytosine to uracil [152]. *In vitro* studies have demonstrated the further ability of AID/APOBEC to deami‐ nate 5mC in DNA, to thymine, resulting in a T:G mismatch [149]. The excision conducted by a TDG glycosylase would subsequently result in an abasic site (apurinic and apyrimidinic [AP] site) which would then be subject to repair by BER. The final product of such a chain reaction would be the regeneration of cytosine in place of the modified base [149].

There are a number of variations and caveats of this and related processes. For instance, AID and APOBEC have frequently been seen to function in a single-stranded DNA environment [149]. Deamination in single-stranded DNA has been experimentally observed *in vitro* and in an *E. coli* assay [149]. Despite this, AID and APOBEC are both present at appreciable levels in oocytes as well as PGCs, so their potential role in developmental demethylation has not been dismissed [149].

An alternate pathway through which AID/APOBEC are thought to function involves the deamination of 5hmC to 5-hydroxymethyluracil (5hmU) and its subsequent removal by a TDG glycosylase or BER pathway [153]. This process would result in the eventual replacement by cytosine. The over-expression of TET1 and AID have been observed to lead to a global accumulation of 5hmU [153]. Two potential pathways may compete with one another because both TDG as well as selective monofunctional uracil-DNA glycosylase 1 (SMUG1) have strong affinity towards the mismatch that would be generated upon deamination: G:hmU [153, 154]. Hence, one of these mechanisms is thought to play a vital role in mediating the downstream commencement of BER following 5mC hydroxylation. Such observations substantiate what many studies propose: that TDG plays an absolutely essential role in active demethylation, regardless of what mechanism succeeds it.

[140]. Scientists continue to ponder the other biological effects which would result from rapid

Epigenetic Mechanisms of the Vascular Endothelium

http://dx.doi.org/10.5772/58569

19

Quite clearly, numerous potential active demethylation pathways do exist and the validity of one over the other is constantly being reassessed. Further oxidation to 5fC or 5caC, direct removal of the methyl group, AID/APOBEC, TDG, and BER pathways have all been proposed and are now under scientific scrutiny. Numerous sources highlight the possibility of more than

Lethargy, extreme muscle and joint pain, gum disease, loosening of teeth, and emotional instability. Often mistaken for syphilis, leprosy, or dysentery, such were the symptoms that characterized "the plague of the sea" [159].Now a rare disease, scurvy took the lives of twothirds of Vasco de Gama's men, eighty per cent of Magellan's mates, and terrorized many of those who took to the sea during the Age of Exploration. Little did the famed 15th century explorers know that they were losing members of their crew to a vitamin deficiency. Sailors who boarded ships destined for long journeys relied mainly on cured and salted meats as well as dried grains, and suffered greatly for their deprivation of perishable fruits and vegetables. It was not until its identification and isolation in the 1930s that the association between vitamin C (ascorbate) and its role in scurvy was made. In fact, ascorbic acid, from which the L-

Unlike many animals, primates, humans, guinea pigs, and a few varieties of fish, cannot synthesize vitamin C *de novo* in the liver [161]. In humans, for instance, the final step of vitamin C biosynthesis cannot be performed: the conversion of L-gulono-gamma-lactone into ascorbic acid. The gene that encodes gulonolactone, the enzyme which catalyzes this reaction, is present in the human genome, but is inactive as a result of mutation accumulation that turned it into a pseudogene [162]. Vitamin C is known to be a critical component of health, while lack of it is truly a detriment to the body because of its dual function in a number of enzymatic reactions

Without a doubt, vitamin C presence is absolutely vital in the regular synthesis of collagen. Being the most abundant protein in mammals and composed mainly of connective tissue [163], the triple helical construction of collagen requires the successful completion of a number of biochemical events. One of these is the essential enzymatic hydroxylation of proline (Pro) residues into hydroxyproline (Hyp) by prolyl-4-hydroxylase (P4H) [164]. A member of a dioxygenase superfamily, P4H decarboxylates the co-substrate, α-ketoglutarate, and utilizes Fe2+as a co-factor, yielding hydroxyproline and an oxidized Fe3+[165]. For full catalytic activity, ascorbate is required as another co-factor in the reaction [166, 167]. In the absence of ascorbate,

one of these pathways operating simultaneously with one or more of the others.

enantiomer, ascorbate, is derived, actually means "anti-scurvy" [160].

SAM level fluctuations.

**4. Case study I: vitamin C**

as well as its role as an antioxidant.

**4.2. Collagen biosynthesis**

**4.1. Scurvy**

Perhaps what could be considered the downfall of the AID/APOBEC pathway was elucidated in a series of experiments and simulations conducted by Nabel *et al*. [152]. Insisting that the role of this deamination-based mechanism is limited, the researchers examined the plausibility of this pathway by investigating the biochemistry of natural and non-natural modified cytosines. The series of substrates represented a 150 fold difference in reactivity, with the size of the substituent being an integral determinant of susceptibility to deamination. At one end of the scale was unmodified cytosine, the behavior of which as a deaminase substrate was unequivocally superior to all other larger natural and unnatural substrates. The bulky 5hmC not only sterically hindered the activity of AID/APOBEC, but its poor hydrophobic character was also implicated in substantially decreasing its reactivity, in comparison to all other bases. The researchers consolidated their results and firmly stated that AID/APOBEC family members preferentially deaminate unmodified cytosine, yet strongly discriminate against any and all 5-substituted cytosine substrates [152]. Clearly, this result contradicts the notion of 5hmC deamination to 5hmU, and more so favours the other possibility of 5mC deamination to thymine. The hope is that future research will work towards eliminating such discrepancies amongst multiple lines of work as we gain a better understanding of the plausibility of these pathways.

#### *3.1.5. DNMT dehydroxymethylation*

In addition to AID and APOBEC, the activity of DNMTs themselves has recently been proposed as a possible 5mC demethylation mechanism. In 2012, Chen *et al.* demonstrated that DNMT enzymes can remove the hydroxymethyl group of 5hmC *in vitro* [155]. Hence, 5hmC is directly converted to cytosine [156]. Although it is still unknown whether such a reaction takes place in cells [84], it has been established that reducing conditions favour the generally accepted methyltransferase activity of DNMT3A and 3B while oxidizing conditions are ideal for dehydroxymethylation activity [155]. Participation in both methylation and demethylation results in rapid cycling between the removal and replacement of methylation patterns – a phenomenon that has been reported in two papers to date [157, 158]. In spite of our analysis of a limited number of experiments, both papers refer to the interplay of TDG and BER in this transcriptional cycling. Particular repair proteins were, in fact, recruited to site-specific locations, likely assisting in the reconstruction of the site [140]. Physiological implications must also be taken into account. S-adenosylmethionine (SAM) is required, not only at low levels for the DNMT3A/B mediated reaction, but also at specific levels for other biochemical reactions [140]. Scientists continue to ponder the other biological effects which would result from rapid SAM level fluctuations.

Quite clearly, numerous potential active demethylation pathways do exist and the validity of one over the other is constantly being reassessed. Further oxidation to 5fC or 5caC, direct removal of the methyl group, AID/APOBEC, TDG, and BER pathways have all been proposed and are now under scientific scrutiny. Numerous sources highlight the possibility of more than one of these pathways operating simultaneously with one or more of the others.

## **4. Case study I: vitamin C**

#### **4.1. Scurvy**

glycosylase or BER pathway [153]. This process would result in the eventual replacement by cytosine. The over-expression of TET1 and AID have been observed to lead to a global accumulation of 5hmU [153]. Two potential pathways may compete with one another because both TDG as well as selective monofunctional uracil-DNA glycosylase 1 (SMUG1) have strong affinity towards the mismatch that would be generated upon deamination: G:hmU [153, 154]. Hence, one of these mechanisms is thought to play a vital role in mediating the downstream commencement of BER following 5mC hydroxylation. Such observations substantiate what many studies propose: that TDG plays an absolutely essential role in active demethylation,

Perhaps what could be considered the downfall of the AID/APOBEC pathway was elucidated in a series of experiments and simulations conducted by Nabel *et al*. [152]. Insisting that the role of this deamination-based mechanism is limited, the researchers examined the plausibility of this pathway by investigating the biochemistry of natural and non-natural modified cytosines. The series of substrates represented a 150 fold difference in reactivity, with the size of the substituent being an integral determinant of susceptibility to deamination. At one end of the scale was unmodified cytosine, the behavior of which as a deaminase substrate was unequivocally superior to all other larger natural and unnatural substrates. The bulky 5hmC not only sterically hindered the activity of AID/APOBEC, but its poor hydrophobic character was also implicated in substantially decreasing its reactivity, in comparison to all other bases. The researchers consolidated their results and firmly stated that AID/APOBEC family members preferentially deaminate unmodified cytosine, yet strongly discriminate against any and all 5-substituted cytosine substrates [152]. Clearly, this result contradicts the notion of 5hmC deamination to 5hmU, and more so favours the other possibility of 5mC deamination to thymine. The hope is that future research will work towards eliminating such discrepancies amongst multiple lines of work as we gain a better understanding of the plausibility of these

In addition to AID and APOBEC, the activity of DNMTs themselves has recently been proposed as a possible 5mC demethylation mechanism. In 2012, Chen *et al.* demonstrated that DNMT enzymes can remove the hydroxymethyl group of 5hmC *in vitro* [155]. Hence, 5hmC is directly converted to cytosine [156]. Although it is still unknown whether such a reaction takes place in cells [84], it has been established that reducing conditions favour the generally accepted methyltransferase activity of DNMT3A and 3B while oxidizing conditions are ideal for dehydroxymethylation activity [155]. Participation in both methylation and demethylation results in rapid cycling between the removal and replacement of methylation patterns – a phenomenon that has been reported in two papers to date [157, 158]. In spite of our analysis of a limited number of experiments, both papers refer to the interplay of TDG and BER in this transcriptional cycling. Particular repair proteins were, in fact, recruited to site-specific locations, likely assisting in the reconstruction of the site [140]. Physiological implications must also be taken into account. S-adenosylmethionine (SAM) is required, not only at low levels for the DNMT3A/B mediated reaction, but also at specific levels for other biochemical reactions

regardless of what mechanism succeeds it.

18 Epigenetics and Epigenomics

pathways.

*3.1.5. DNMT dehydroxymethylation*

Lethargy, extreme muscle and joint pain, gum disease, loosening of teeth, and emotional instability. Often mistaken for syphilis, leprosy, or dysentery, such were the symptoms that characterized "the plague of the sea" [159].Now a rare disease, scurvy took the lives of twothirds of Vasco de Gama's men, eighty per cent of Magellan's mates, and terrorized many of those who took to the sea during the Age of Exploration. Little did the famed 15th century explorers know that they were losing members of their crew to a vitamin deficiency. Sailors who boarded ships destined for long journeys relied mainly on cured and salted meats as well as dried grains, and suffered greatly for their deprivation of perishable fruits and vegetables. It was not until its identification and isolation in the 1930s that the association between vitamin C (ascorbate) and its role in scurvy was made. In fact, ascorbic acid, from which the Lenantiomer, ascorbate, is derived, actually means "anti-scurvy" [160].