Preface

Chapter 9 **Cytosine Modifications and Distinct Functions of TET1 on**

Chapter 10 **Role of COX-2 Promoter Methylation and Helicobacter pylori Infection in Impaired Gastric Ulcer Healing 207**

Chapter 11 **Epigenetic Regulation of Hepatitis B Virus Replication 223**

In Young Moon and Jin-Wook Kim

Chapter 12 **Part 1: The PIWI-piRNA Pathway Is an Immune-Like**

**Silencing Transposable Elements 233** Didier Meseure and Kinan Drak Alsibai

Didier Meseure and Kinan Drak Alsibai

Hiroshi Yasuda, Yoshiyuki Watanabe, Ritsuko Oikawa and Fumio

**Surveillance Process That Controls Genome Integrity by**

**New Candidate Biomarkers and Potential Therapeutic Tools**

Chapter 13 **Part 2: Deregulated Expressions of PIWI Proteins and piRNAs as**

Cuili Ma, Pengfei Ji, Nina Xie and Yujing Li

**Tumorigenesis 187**

Itoh

**VI** Contents

**in Cancer 263**

Since Charles Darwin put forward his famous bottom-up theory of natural selection in "The Origin of Species" in 1859, genetics and nowadays genomics increasingly gained world-wide attention [1]. The frequently debated cartoons depicting the descent of man from apes mark the transition from ancient mystical beliefs to a scientifically falsifiable modern theory of the origin of life and mankind. Jean-Baptiste Lamarck had already put forward a top-down hypothesis in 1809 in his famous book "Philosophie Zoologique" symbolized by the elongating giraffe-neck longing for leaves at tree-tops [2]. It achieved public attention due to the 'motivated change' paradigm that remains simple to grasp, actually to this day. The discovery of the DNA double helix and the four base code culminated in the publicly much anticipated race to decipher the sequence of the human genome in 2002 by the public Human Genome Project and the private initiative of Craig Venter. Now everything would be known about humans, their lives from birth to death as well as all species, the origin of life and its future - so resounded the promise of some and the happy belief of many.

But are 3 billion A, T, G, C bases and the ensuing code for ~20,000 proteins really sufficient explanation for the holy grail of human life, as would be suggested by monozygotic twin physiologic and physiognomic identity? Or is the real situation much more complex, potentially involving a multitude of interactions of the genotype ranging from its own internal physicochemical foundation, via the phenotype it is creating, up to the entire ecosystem, which is itself made up of many genomes? There is little doubt that a purely reductionistic approach cannot explore the full extent of the interaction-networks of genomes. While reductionism can formally identify biological variables that are rate-limiting *under* the experimental conditions that are tested, there may always be biological signals that are not observed because they were not solicited during the experiment.

Since the initial investigations in the late 18th century much progress has been made, achieving a picture of the notoriously hard-to-access eukaryotic cell nucleus and the chromatin it contains [3]. This revealed a layered organization of the physical genome comprising DNA, nucleosomes, chromatin quasi-fibres, chromatin loops, loop aggregates/rosettes, as well as chromosome arms, entire chromosomes, and their position within the cell nucleus as outlined in Chapter 4 of this book.

Intriguingly, it also has become apparent relatively early already that there are heritable phenotype changes that do not involve alterations in the nucleotide sequence. This led to the concept of epigenetic coding initially introduced by Conrad Hall Waddington in 1942 [4] to explain why almost every cell of an organism harbours the same DNA but does not express the same parts of the genetic information, enabling cell fate determination and cell lineage differentiation to yield all the cells of an organism, as explained in Chapter 1.

This book addresses current issues in the fields of epigenetics and chromatin ranging from more theoretical overviews in the first four chapters to much more detailed methodologies and insights into diagnostics and treatments in the other chapters.

In the elaborate Chapter 1 *"Logic of Epigenetics and Investigation of Potential Gene Regions"*, an overview is presented on epigenetic coding and the regulation of genes as well as what kind of modifications appear and how this can be understood within a broader scope. Chapter 2 *"Recognition of Nucleosomes by Chromatin Factors: Lessons from Data-Driven Docking-Based Structures of Nucleosome-Protein Complexes"* focuses on the intricate molecular interactions and thus how epigenetics actually works, i.e. the involved proteins and their structure. In Chapter 3 *"Chromatin Dynamics Upon DNA Damage"*, fingers are laid deep into the chromatin dynamics after DNA damage and its repair, thus showing how a genome reacts to the inevitable reality of life and consequent DNA damaging events. Finally, this first part of the book is rounded-off by Chapter 4 *"A Consistent Systems Mechanics Model of the 3D Architecture and Dynamics of Genomes"*, in which for the first time a broad systems genomics model based on the complete determination of genomic layers is presented leading to new perspectives on genome evolution and general complex systems development in nature.

As far as much more detailed methodologies and insights are concerned, in Chapter 5 *"Apicomplexan and Histone Variants: What's new?"*, the clinically relevant histone variants in Plasmodium spp. and Toxoplasma gondii are investigated in depth. Furthermore, in the far-reaching Chapter 6 *"Epigenetic Modulation of Circadian Rhythms: Bmal1 Gene Regulation"*, regulation of complex metabolic effects and phenotypic modulations are considered within a disease-relevant context. In Chapter 7 *"Epigenome Editing"*, we dive deeply into an overview of modern epigenome editing systems locally and in genome-wide contexts, of which the CRISPR-Cas9 system has gained prominent public attention. This leads immediately to Chapter 8 *"Resetting Cell Fate by Epigenetic Reprogramming"*, which details phenomenally the setting of epigenetic patterns during differentiation and different reprogramming strategies that can be applied. In Chapter 9 *"Cytosine Modifications and Distinct Functions of TET1 on Tumorigenesis*", very practical aspects of epigenetics during tumorigenesis are investigated. Other important clinical aspects are considered in Chapter 10 *"Role of COX-2 Promoter Methylation and Helicobacter pylori Infection in Impaired Gastric Ulcer Healing"*, where a treatment of epigenetic inhibition is shown. In the broad Chapter 11 *"Epigenetic Regulation of Hepatitis B Virus Replication"*, the importance of epigenetics for the regulation of the Hepatitis B virus is described, thus shedding light on how epigenetic control of transcription can be used for therapeutic strategies. The book ends with a great double: In Chapter 12 *"Part 1: The PIWI-piRNA Pathway is an Immune-Like Surveillance Process that Controls Genome Integrity by Silencing Transposable Elements"*, we get an in-depth introduction into the pivotal roles of the PIWI pathway focusing on origin, properties, and functions in the germ line and somatic tissues. This is followed by Chapter 13 *"Part 2: Deregulated Expressions of PIWI Proteins and piRNAs as New Candidate Biomarkers and Potential Therapeutic Tools in Cancer"*, where we dive into how such epigenetic-based research as in the case of PIWI can lead to biomarkers which could be used as potential therapeutic tools in the perhaps emotionally most feared disease, namely cancer.

Consequently, the general development of genomics, which these chapters on epigenetics and chromatin illustrate in both their depth as well as broadness, shows clearly that genetic information is stored on all structural and dynamical levels within the nucleus with corresponding modifications. Only an integrative systems approach allows to understand and manipulate the consequently holistic interplay of geno- and phenotype creating functional genomes. All this opens the door to a concrete grasp of life as well as in more general terms complex systems as a whole. Hence, genomics and the entire biology are driven into the future by broad complex physical and mathematical methodologies and approaches. This not only opens

**III**

existence.

**Figure 1.**

*genomics entanglement.*

opportunities for a true universal view of genetic information, but also is the key for a general understanding of genomes, their function, as well as life and evolution in general. Furthermore, these insights pave the path for diagnostics and disease treatment, for future genome manipulation and engineering efforts, and ultimately also for *de novo* created life forms. This will leave much room for new ample opportuni-

*Visions make the world go round: The simulation of an entire human genome with all chromosomes (different colours; [5]) depicting a chromatin quasi-fibre folding into stable loop aggregates/rosettes (Multi-Loop Subcompartment Model) has opened huge opportunities for an immediate intuitive understanding of the dynamic genome organization and function not only as, i.e. concerned spatial stable proximities, accessibilities, and replicability are concerned, but also in respect to the bigger genotype-phenotype evolutionary systems* 

Thus, in practical terms and in the formulation of T.A.K., to ultimately approach Sustainable Development Goals as health/disease, and death, i.e. to achieve "eternal" as well as artificial intelligence and life, demands the following: i) R&D *must* work inter-/trans-disciplinarily in an open innovative network! Here, *THE* keys are new virtual paper tools representing and seamlessly visualizing, integrating, and manipulating the complexity of systems wholeness (Figure 1, 2; Movie 1). Beyond, as foundation, ii) broad humanistic education (the baroquian *Bildung* ideal) *must* be achieved with inter-/trans-disciplinary curricula of *ALL* sciences, arts, and professional crafts to efficiently exploit the opportunities of systems complexity. Learning for its own sake beyond mere training on the job *must* be the final mantra. Lastly, of ultimate importance, iii) society as a whole *must* epitomize an overall integrative thinking and operation, i.e. living an internalized Human Ecology autopoietic systems perspective [10]. Hence, *ALL* this *must* be represented in a humanistic systems vision of terrestrial, interplanetary, and artificial intelligence/life, being for everybody *ad hoc* graspable in a playful "Glass Bead Game" [11] manner, both for the detailed daily practice as well as for a general "enlightened" understanding of

ties and we are sure that the most interesting times are yet to come.

#### **Figure 1.**

*Visions make the world go round: The simulation of an entire human genome with all chromosomes (different colours; [5]) depicting a chromatin quasi-fibre folding into stable loop aggregates/rosettes (Multi-Loop Subcompartment Model) has opened huge opportunities for an immediate intuitive understanding of the dynamic genome organization and function not only as, i.e. concerned spatial stable proximities, accessibilities, and replicability are concerned, but also in respect to the bigger genotype-phenotype evolutionary systems genomics entanglement.*

opportunities for a true universal view of genetic information, but also is the key for a general understanding of genomes, their function, as well as life and evolution in general. Furthermore, these insights pave the path for diagnostics and disease treatment, for future genome manipulation and engineering efforts, and ultimately also for *de novo* created life forms. This will leave much room for new ample opportunities and we are sure that the most interesting times are yet to come.

Thus, in practical terms and in the formulation of T.A.K., to ultimately approach Sustainable Development Goals as health/disease, and death, i.e. to achieve "eternal" as well as artificial intelligence and life, demands the following: i) R&D *must* work inter-/trans-disciplinarily in an open innovative network! Here, *THE* keys are new virtual paper tools representing and seamlessly visualizing, integrating, and manipulating the complexity of systems wholeness (Figure 1, 2; Movie 1). Beyond, as foundation, ii) broad humanistic education (the baroquian *Bildung* ideal) *must* be achieved with inter-/trans-disciplinary curricula of *ALL* sciences, arts, and professional crafts to efficiently exploit the opportunities of systems complexity. Learning for its own sake beyond mere training on the job *must* be the final mantra. Lastly, of ultimate importance, iii) society as a whole *must* epitomize an overall integrative thinking and operation, i.e. living an internalized Human Ecology autopoietic systems perspective [10]. Hence, *ALL* this *must* be represented in a humanistic systems vision of terrestrial, interplanetary, and artificial intelligence/life, being for everybody *ad hoc* graspable in a playful "Glass Bead Game" [11] manner, both for the detailed daily practice as well as for a general "enlightened" understanding of existence.

**II**

In the elaborate Chapter 1 *"Logic of Epigenetics and Investigation of Potential Gene Regions"*, an overview is presented on epigenetic coding and the regulation of genes as well as what kind of modifications appear and how this can be understood within a broader scope. Chapter 2 *"Recognition of Nucleosomes by Chromatin Factors: Lessons from Data-Driven Docking-Based Structures of Nucleosome-Protein Complexes"* focuses on the intricate molecular interactions and thus how epigenetics actually works, i.e. the involved proteins and their structure. In Chapter 3 *"Chromatin Dynamics Upon DNA Damage"*, fingers are laid deep into the chromatin dynamics after DNA damage and its repair, thus showing how a genome reacts to the inevitable reality of life and consequent DNA damaging events. Finally, this first part of the book is rounded-off by Chapter 4 *"A Consistent Systems Mechanics Model of the 3D Architecture and Dynamics of Genomes"*, in which for the first time a broad systems genomics model based on the complete determination of genomic layers is presented leading to new perspectives on genome evolution and general complex

As far as much more detailed methodologies and insights are concerned, in Chapter 5 *"Apicomplexan and Histone Variants: What's new?"*, the clinically relevant histone variants in Plasmodium spp. and Toxoplasma gondii are investigated in depth. Furthermore, in the far-reaching Chapter 6 *"Epigenetic Modulation of Circadian Rhythms: Bmal1 Gene Regulation"*, regulation of complex metabolic effects and phenotypic modulations are considered within a disease-relevant context. In Chapter 7 *"Epigenome Editing"*, we dive deeply into an overview of modern epigenome editing systems locally and in genome-wide contexts, of which the CRISPR-Cas9 system has gained prominent public attention. This leads immediately to Chapter 8 *"Resetting Cell Fate by Epigenetic Reprogramming"*, which details phenomenally the setting of epigenetic patterns during differentiation and different reprogramming strategies that can be applied. In Chapter 9 *"Cytosine Modifications and Distinct Functions of TET1 on Tumorigenesis*", very practical aspects of epigenetics during tumorigenesis are investigated. Other important clinical aspects are considered in Chapter 10 *"Role of COX-2 Promoter Methylation and Helicobacter pylori Infection in Impaired Gastric Ulcer Healing"*, where a treatment of epigenetic inhibition is shown. In the broad Chapter 11 *"Epigenetic Regulation of Hepatitis B Virus Replication"*, the importance of epigenetics for the regulation of the Hepatitis B virus is described, thus shedding light on how epigenetic control of transcription can be used for therapeutic strategies. The book ends with a great double: In Chapter 12 *"Part 1: The PIWI-piRNA Pathway is an Immune-Like Surveillance Process that Controls Genome Integrity by Silencing Transposable Elements"*, we get an in-depth introduction into the pivotal roles of the PIWI pathway focusing on origin, properties, and functions in the germ line and somatic tissues. This is followed by Chapter 13 *"Part 2: Deregulated Expressions of PIWI Proteins and piRNAs as New Candidate Biomarkers and Potential Therapeutic Tools in Cancer"*, where we dive into how such epigenetic-based research as in the case of PIWI can lead to biomarkers which could be used as potential therapeutic tools in the perhaps emotionally most feared disease, namely cancer.

Consequently, the general development of genomics, which these chapters on epigenetics and chromatin illustrate in both their depth as well as broadness, shows clearly that genetic information is stored on all structural and dynamical levels within the nucleus with corresponding modifications. Only an integrative systems approach allows to understand and manipulate the consequently holistic interplay of geno- and phenotype creating functional genomes. All this opens the door to a concrete grasp of life as well as in more general terms complex systems as a whole. Hence, genomics and the entire biology are driven into the future by broad complex physical and mathematical methodologies and approaches. This not only opens

systems development in nature.

#### **Figure 2, Movie 1.**

*Practical systemic virtual paper tools make seeing is believing accessible: The GLOBE 3D Genome Platform [6] creates a virtual desktop environment for genomics combining i) visual data representation, ii) data access/ management, and iii) data analysis/creation. This allows, i.e. to combine 3D genome simulations (background left [5]) with complex DNA similarity and syndrome analysis of a linear ideogram chromosome representation (foreground) in respect to actual data (microscopy/FISH of two chromosome loci: PWLS/AS region (A-C; [5, 7]), chromosome arms (D; courtesy S. Dietzel), subchromosomal domains (E; courtesy D. Zink) [5], IgH region (F, G; [8]; T2C chromosomal interaction maps, (H, I; [9]), allowing complexity to be intuitively approached systemically.*

Last but not least, we would like to point out the unusually long history of this book which initially started as two separate titles: "Chromatin" has been edited by Dr. Colin Logie since autumn 2017 and "Epigenetics" edited originally by Dr. Hasibe Cingilli Vural, from the Necmettin Erbakan University Meram Medicine Faculty, Turkey, in October 2017. Dr. Vural collected a phenomenal set of chapters, but due to circumstances not in her hands had to resign from her editorship. With everything on stake, Dr. Tobias A. Knoch (already a contributor) offered to take over the editorship of Dr. Vural. Over the course of time by the odds of life, Dr. Tobias A. Knoch, also contributor to the "Chromatin" book, and Dr. Colin Logie decided to join forces and combine the books into *"Chromatin and Epigenetics"*, of which you now hold the result in your hands.

Thus, we also would like to thank all the authors for their cooperation and patience.

During this project, it was a pleasure for us to work with IntechOpen Publisher. We would like to express our appreciation to all members of this team participating in this effort, especially Author Service Managers Danijela Sakić, Romina Rovan and Edi Lipović, as well as Commissioning Editor Andrea Korić.

> **Dr. Colin Logie and Dr. Tobias A. Knoch** Nijmwegen/Rotterdam, The Netherlands, November 2019

> > **V**

**Video**

1859

1809

**Cover image**

**References**

Video file available from: https://bit.ly/37KBTgU

[1] Darwin CR. On the origin of species.

[2] Lamarck J-B. Philosophie Zoologique.

[3]Cremer T, Cremer C. Centennial of Wilhelm Waldeyer's introduction of the term"chromosome" in 1888. Cytogenetics and Cell Genetics.1988;**48**(2):65-67

[4] Waddington CH. The epigenotype.

[5] Knoch TA. Approaching the threedimensional organization of the human genome: Structural-, scaling- and dynamic properties in the simulation of interphase chromosomes and cell nuclei, long-range correlations in complete genomes, *in vivo* quantification of the chromatin distribution,

construct conversions in simultaneous co-transfections. Mannheim, Germany: TAKPress; 2002. ISBN 3-00-009959-X

[6] Knoch TA, Lesnussa M, Kepper FN, Eussen HB, Grosveld FG. The GLOBE 3D Genome Platform—Towards a novel system-biological paper tool to integrate

[7] Rauch J, Knoch TA, Solovei I, Teller K, Stein S, Buiting K, et al. Lightoptical precision measurements of the

the huge complexity of genome organization and function. Studies in Health Technology and Informatics.

2009;**147**:105-116

Endeavour. 1942;**1**:18-20

Simulation of an entire human genome with all chromosomes (different colours) depicting a chromatin quasi-fibre folding into stable loop aggregates/rosettes (Multi-Loop Subcompartment Model); with courtesy of Dr. Tobias A. Knoch (for more details see Figure 1 of the Preface and there literature [5], or Chapter 5 and references therein).

> Prader-Willi/Angelman Syndrome imprinting locus in human cell nuclei indicate maximum condensation changes in the few hundred nanometer range. Differentiation. 2008;**76**(1):66-82

[8] Jhunjhunwala S, van Zelm MC, Peak MM, Cutchin S, Riblet R, van Dongen JJM, et al. The 3D-structure of the immunoglobulin heavy chain locus: implications for long-range genomic interactions. Cell. 2008;**133**(2):265-279

[9] Knoch TA, Wachsmuth M, Kepper N,

[10] Knoch TA. Sustained renewability: Approached by systems theory and human ecology. In M. Nayeripour M, Keshti M, editors. Renewable Energy Sources. Vol. 2. IntechOpen. 2011. pp. 21-48. ISBN 978-953- 307-573-0. Available at: https:// www.intechopen.com/books/

sustainable-growth-and-applications-

sustainedrenewability-approached-bysystems-theory-and-human-ecology

[11] Hesse H. The Glass Bead Game. Holt, Rinehart and Winston, New York;

in-renewable-energy-sources/

Lesnussa M, Abuseiris A, Imam AMA, et al. The detailed 3D multiloop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes. Epigenetics & Chromatin.

2016;**58**(9):1-22

1943
