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## IntechOpen Book Series Biochemistry Volume 15

Metin Budak, MSc, PhD is an Assistant Professor at Trakya University, Faculty of Medicine. He has been Head of the Molecular Research Lab at Prof. Mirko Tos Ear and Hearing Research Center since 2018. His specializations are biophysics, epigenetics, genetics, and methylation mechanisms. He has published around 23 peer-reviewed papers, 2 book chapters, and 28 abstracts. He is a member of the Clinical Research Ethics Committee and Quantifi-

cation and Consideration Committee of Medicine Faculty. His research area is the role of methylation during gene transcription, chromatin packages DNA within the cell and DNA repair, replication, recombination, and gene transcription. His research focuses on how the cell overcomes chromatin structure and methylation to allow access to the underlying DNA and enable normal cellular function.

Mustafa Yildiz is a researcher in the Department of Biophysics, Faculty of Medicine, Trakya University. He holds a BSc degree from Sakarya University (2009) and an MSc degree from Trakya University (2016). He quickly became interested in epigenetic control of gene expression which governs virtually all cellular processes such as proliferation, development, differentiation, and interaction with the environment. During his master's thesis, he

studied gene expression changes in the exposure of nanoparticles and he investigated how different signaling pathways regulate genes in human cells after photodynamic therapy. He has published over 8 articles in refereed journals, 1 chapter and 32 abstracts in scientific meetings.

**Editors of Volume 15: Metin Budak and Mustafa Yildiz** Trakya University, Turkey

**Book Series Editor: Miroslav Blumenberg** NYU Langone Medical Center, New York, USA

### Scope of the Series

Contents

**Section 1**

**Section 2**

*by Metin Budak*

**Preface XI**

Environmental Factors in Methylation Mechanisms **1**

**Chapter 1 3**

Methylation Mechanisms in Embryonic Period **19**

**Chapter 2 21**

**Chapter 3 39**

**Chapter 4 61**

Methylation Mechanisms in Process of Cancer **75**

**Chapter 5 77**

**Chapter 6 97**

Demethylation in Early Embryonic Development and Memory

Global DNA Methylation as a Potential Underlying Mechanism

Recent Insights into the Mechanisms of *De Novo* and Maintenance of

DNA Hydroxymethylation in the Regulation of Gene Expression

*Nicolás Serafín-Higuera, Silvia García, Claudia E. Millán-Testa,* 

Research Progress of DNA Methylation in Thyroid Cancer

*Mónica Sierra-Martínez, Magali Blanco-Morales and Jorge Sandoval-Basilio*

*by Sofia L. Alcaraz-Estrada, Gabriela Leija-Montoya,* 

Radiation and DNA Methylation Mechanisms

*by Carol Bernstein and Harris Bernstein*

of Congenital Disease Development

DNA Methylation in Mammals

*by Aleksandra Stanković*

in Human Solid Cancer

*by Zhu Gaohong and Xie Lijun*

*by Motoko Unoki*

**Section 3**

Biochemistry, the study of chemical transformations occurring within living organisms, impacts all of life sciences, from molecular crystallography and genetics, to ecology, medicine and population biology. Biochemistry studies macromolecules proteins, nucleic acids, carbohydrates and lipids –their building blocks, structures, functions and interactions. Much of biochemistry is devoted to enzymes, proteins that catalyze chemical reactions, enzyme structures, mechanisms of action and their roles within cells. Biochemistry also studies small signaling molecules, coenzymes, inhibitors, vitamins and hormones, which play roles in the life process. Biochemical experimentation, besides coopting the methods of classical chemistry, e.g., chromatography, adopted new techniques, e.g., X-ray diffraction, electron microscopy, NMR, radioisotopes, and developed sophisticated microbial genetic tools, e.g., auxotroph mutants and their revertants, fermentation etc. More recently, biochemistry embraced the 'big data' omics systems.

Initial biochemical studies have been exclusively analytic: dissecting, purifying and examining individual components of a biological system; in exemplary words of Efraim Racker, (1913 - 1991) "Don't waste clean thinking on dirty enzymes." Today however, biochemistry is becoming more agglomerative and comprehensive, setting out to integrate and describe fully a particular biological system. The "big data" metabolomics can define the complement of small molecules, e.g., in a soil or biofilm sample; proteomics can distinguish all the proteins comprising e.g., serum; metagenomics can identify all the genes in a complex environment e.g., bovine rumen. This Biochemistry Series will address both the current research on biomolecules, and the emerging trends with great promise.

## Contents



Preface

DNA, which is the basic determinant of life, is a molecule that has very interesting properties and can be complex and simple simultaneously. Since Watson and Crick, who discovered the molecular structure of DNA, we still continue to

The purpose of this book is to cover the mechanisms of action of epigenetic changes in different living species while also looking at the environmental factors, cancer, and embryonic life for a better understanding of epigenetic changes. It is also to create a resource book that can appeal to people from many different fields of science, from

**Metin Budak and Mustafa Yildiz** 

Trakya University,

Turkey

beginners to professionals, to investigate epigenetic mechanisms.

One of these interesting features of DNA is epigenetic modifications. Noninherited molecular changes that occur without any change in DNA sequence are called "epigenetics". Epigenetics, the existence of which was known before Watson and Crick, was first described by Conrad Waddington in 1942 as phenotypic changes caused by the relationship between gene and gene products. Although it was then thought to be related to cell division only, it has been shown that epigenetic processes can be passed on to the next generations. It is now known to have a similar functioning in yeasts, fruit flies, mice, humans, and especially plants. The genome is the sum of genetic information in the DNA sequence of a cell/organism. The epigenome is when a cell/organism regulates gene expression independently from the DNA sequence by chemical modifications of DNA and histone molecules.

understand DNA.

*by Kendall R. Corbin and Carlos M. Rodriguez Lopez*
