Preface

Chapter 7 **Chromatin Remodeling in DNA Damage Response and**

Chapter 8 **Chromatin Remodelling During Host-Bacterial Pathogen**

Yong Zhong Xu, Cynthia Kanagaratham and Danuta Radzioch

Lili Gong, Edward Wang and Shiaw-Yih Lin

**Human Aging 153**

**Interaction 173**

Daniela Zahorakova

Chapter 9 **Rett Syndrome 199**

**VI** Contents

In the eukaryotic cells, DNA, histone proteins and associated macromolecules are tightly packaged into chromatin. The basic unit of chromatin is the nucleosome – a DNA fragment wrapped around an octamer core of histone proteins. During the past two decades the field of chromatin research has advanced at an incredible pace due to the development of novel techniques. It has become increasingly clear that, rather than simply representing packaged DNA, chromatin organization undergoes dynamic changes and plays a key role in control‐ ling genome activities throughout life, from the onset of embryonic development to cell, tis‐ sue and organ differentiation. The term "chromatin remodelling" is widely used to describe changes in chromatin structure which is controlled by histone-modifying enzymes, chroma‐ tin remodelling complexes, non-histone DNA-binding proteins and noncoding RNAs. Many human diseases such as cancer, various genetic syndromes, autism and infectious disease have been linked to the disruption of these control processes by genetic, environmental or microbial factors. Therefore, to unravel the mechanisms by which they operate is one of the most exciting and rapid developing fields of modern biology and will contribute to new ways in treatment of these diseases.

The chapters in this book will focus on recent advances in our understanding of the mecha‐ nisms that govern the dynamic structural of chromatin, thereby providing important in‐ sights into gene regulation, DNA repair, and human diseases.

The book begins with the section "Molecular basis for chromatin structure and regulation" dealing with the molecular mechanisms underlying chromatin dynamics. In the first chapter "Chromatin Remodelers and Their Way of Action" written by Laura Manelyte and Gernot Langst, the authors give an overview of four major families of chromatin remodelers includ‐ ing SWI/SNF, ISWI, CHD and INO80 family. The domain compositions, components and basic functions of these remodelers have been described and the following three aspects re‐ lated to the functions of chromatin remodelers have been highlighted: 1) Mechanisms of nu‐ cleosome positioning in vitro and in vivo; 2) Targeting of remodelling machines to genomic loci and their specific interaction with the modified substrate and histone variants; 3) Regu‐ lation of remodeler activity. This chapter provides an excellent knowledge in understanding the mechanisms of chromatin remodelling by ATP-dependent chromatin remodelers.

Sumoylation is a post-translational modification of proteins by attachment of the small poly‐ peptide SUMO (small ubiquitin-like modifier), which plays an important role in various cel‐ lular processes, such as nuclear-cytosolic transport, transcriptional regulation, apoptosis, protein stability, signal transduction, cell cycle progression and differentiation. In the second chapter "SUMO Tasks in Chromatin Remodeling" written by Mario Garcia-Dominguez, the prominent function of SUMO in transcriptional regulation, in the context of chromatin struc‐ ture and dynamic, has been discussed. The author describes in detail the different ways by which SUMO is involved in chromatin remodeling: 1) histone modification; 2) modulation of transcription factors activity, and 3) architecture of protein complexes associated to the chro‐ matin, especially those associated to the heterochromatin. This chapter provides a versatile view on molecular mechanisms of chromatin remodeling regulated by sumoylation.

cycle progression, in cancer and in G0-G1 transition in response to mitogenic stimuli are discussed. Id2 is involved in regulation of gene expression as a switch to open or close chromatin structure through modulation of chromatin protein complex at target genes. Fi‐ nally, the molecular regulation of Id2 activity and expression by phosphorylation and GSH

Preface IX

In section 3 "Chromatin remodeling in DNA damage, development and human disease", four chapters are presented, dealing with the molecular mechanisms underlying the in‐ volvement of chromatin remodeling in controlling key physiological or pathological events such as differentiation, development, DNA damage response, tumorigenesis and microbial

Polycomb group (PcG) proteins are highly conserved regulatory factors that were initially discovered in Drosophila. They constitute a global silencing system and play key roles in embryonic development and stem cell maintenance. Deregulation of PcG members contrib‐ ute to defects in stem cell fates and to tumorigenesis. In mammals, PcG proteins form two main complexes: polycomb-repressive complex 1 and 2 (PRC1, PRC2). They act by modify‐ ing chromatin structure and by regulating deposition and recognition of posttranslational

Chapter 6 "Role of Enhancer of Zeste Homolog 2 Polycomb Protein and Its Significance in Tumor Progression and Cell Differentiation" by Irene Marchesi and Luigi Bagella give an overview of molecular biology and function of PCR2 with special emphasis on EZH2, the catalytic subunit of PRC2. The content covers PCR2-mediated silencing mechanism, PCR2 activity regulation, including expression regulation, posttranscriptional modification and re‐ cruitment to target genes, as well as the mechanisms underlying the role of EZH2 in neuro‐

Cells are inescapably and constantly exposed to a variety of environmental and endogenous agents which can cause DNA damage such as single-strand breaks, double-strand breaks, mismatches and base modifications. To maintain genome stability, cells have developed a global signaling network, known as DNA damage response (DDR) to sense and repair DNA damages. Chromatin remodeling is critical during this process, as chromatin constitutes a natural barrier to associated enzymes and regulatory factors to reach DNA. Aging is a com‐ plex process that has long been thought to be a consequence of unprogrammed deleterious events and accumulation of random gene mutation. However, in recent years, DNA damage has been shown to play a central role in premature aging and DNA damage theory of aging has been developed although there are still several unresolved controversies that require

In chapter 7 "Chromatin Remodeling in DNA Damage Response and Human Aging" by Lili Gong, Edward Wang and Shiaw-Yih Lin, the authors summarize the current knowledge on DNA damage repair mechanisms, the role of chromatin remodeling in DDR, DDR in hetero‐ chromatin and the interplay between DNA damage, chromatin remodeling and human ag‐ ing. Intracellular pathogens, through a long-standing coexistence with host cells, have evolved mechanisms that provide pathogens with the amazing capacity to adapt and sur‐ vive in variable and often hostile environments encountered in their hosts. The concept of chromatin modification as a mechanism by which pathogens affect host immune responses

depletion are also discussed.

infection.

histone modifications.

further clarification.

genesis, skeletal myogenesis and tumorigenesis.

to facilitate infection has emerged in recent years.

Chapters 3 to 5 are classified into section 2 "Chromatin remodeling in regulating gene ex‐ pression". It is clear that SW/SNF chromatin remodeling complex plays an important role in the process of RNA polymerase II-mediated transcription. SWI/SNF complex not only as‐ sists transcription events by remodeling nucleosomes but also participates in early event in transcription through interaction with transcription factors and the recruitment of RNA pol‐ ymerase II. Recent studies have suggested that this complex has an activity beyond tran‐ scription initiation as it can regulate the transcription elongation rate with a consequence on alternative splicing. In particular, this complex has been shown to be associated with premRNP. dSWI/SNF complex contains two subcomplexes PBAP and BAP. Which of them is involved in transcription elongation? This question is answered in chapter 3 "SWI/SNF Chromatin Remodeling Complex Involved in RNA Polymerase II Elongation Process in Drosophila Melanogaster" written by authors Nadezhda E. Vorobyeva, Marina U. Mazina and Semen A. Doronin. Chapter 3 is presenting results of an original research. In this article, the authors generated two specific antibodies against OSA and BAP 170, respectively. The OSA is the specific subunit of BAP and the BAP 170 is the specific subunit of PBAP. Using chromatin immunoprecipitation assay, the authors found that both BAP and PBAP subcom‐ plexes bind to the promoter but not to the coding region of ftz-f1 gene before transcription induction. Interestingly, in response to transcription induction, only PBAP but not BAP is found to be accumulated at the coding region of this gene. Similar results are observed when performing the same experiments using another gene (hsp70 gene). Based on these results, the authors suggest that PABP subcomplex is involved in the transcription elonga‐ tion mediated by RNA polymerase II.

In chapter 4 titled "Condensins, Chromatin Remodeling and Gene Transcription", authors Laurence O.W. Wilson and Aude M. Fahrer discuss the role of condensins in the regulation of gene transcription. Condensins belong to an ancient family of protein complexes capable of manipulating chromatin structure. In eukaryotes, condensin I and condensin II are vital for the proper formation and resolution of sister chromosomes. In recent years, evidence has gradually demonstrated that condensins are much more than architects of chromatin struc‐ ture; they are also important regulators of gene transcription. However, the vital role of con‐ densins makes the study of these complexes difficult. In this chapter, the authors introduce several different methods to investigate the roles of condensins in chromatin structure change and gene regulation. A special focus is placed on two particular examples of conden‐ sin in regulating gene transcription: dosage compensation in C. elegans and thymocyte de‐ velopment in mice.

Id2 (inhibitor of DNA binding 2, dominant-negative helix-loop-helix protein) belongs to a family of helix-loop-helix proteins which plays a central role in the regulation of cell growth and differentiation and cancer. In chapter 5 "The Role of Id2 in the Regulation of Chroma‐ tin Structure and Gene Expression" written by Elena R. Garcia-Trevijano, Luis Torres, Rosa Zaragozá and Juan R. Viña, the authors give a broad introduction to the topic. This chap‐ ter begins with description of the structure and functions of Id2 protein followed by the molecular mechanisms underlying the role of Id2 as a proliferative factor in normal cell cycle progression, in cancer and in G0-G1 transition in response to mitogenic stimuli are discussed. Id2 is involved in regulation of gene expression as a switch to open or close chromatin structure through modulation of chromatin protein complex at target genes. Fi‐ nally, the molecular regulation of Id2 activity and expression by phosphorylation and GSH depletion are also discussed.

ture and dynamic, has been discussed. The author describes in detail the different ways by which SUMO is involved in chromatin remodeling: 1) histone modification; 2) modulation of transcription factors activity, and 3) architecture of protein complexes associated to the chro‐ matin, especially those associated to the heterochromatin. This chapter provides a versatile

Chapters 3 to 5 are classified into section 2 "Chromatin remodeling in regulating gene ex‐ pression". It is clear that SW/SNF chromatin remodeling complex plays an important role in the process of RNA polymerase II-mediated transcription. SWI/SNF complex not only as‐ sists transcription events by remodeling nucleosomes but also participates in early event in transcription through interaction with transcription factors and the recruitment of RNA pol‐ ymerase II. Recent studies have suggested that this complex has an activity beyond tran‐ scription initiation as it can regulate the transcription elongation rate with a consequence on alternative splicing. In particular, this complex has been shown to be associated with premRNP. dSWI/SNF complex contains two subcomplexes PBAP and BAP. Which of them is involved in transcription elongation? This question is answered in chapter 3 "SWI/SNF Chromatin Remodeling Complex Involved in RNA Polymerase II Elongation Process in Drosophila Melanogaster" written by authors Nadezhda E. Vorobyeva, Marina U. Mazina and Semen A. Doronin. Chapter 3 is presenting results of an original research. In this article, the authors generated two specific antibodies against OSA and BAP 170, respectively. The OSA is the specific subunit of BAP and the BAP 170 is the specific subunit of PBAP. Using chromatin immunoprecipitation assay, the authors found that both BAP and PBAP subcom‐ plexes bind to the promoter but not to the coding region of ftz-f1 gene before transcription induction. Interestingly, in response to transcription induction, only PBAP but not BAP is found to be accumulated at the coding region of this gene. Similar results are observed when performing the same experiments using another gene (hsp70 gene). Based on these results, the authors suggest that PABP subcomplex is involved in the transcription elonga‐

In chapter 4 titled "Condensins, Chromatin Remodeling and Gene Transcription", authors Laurence O.W. Wilson and Aude M. Fahrer discuss the role of condensins in the regulation of gene transcription. Condensins belong to an ancient family of protein complexes capable of manipulating chromatin structure. In eukaryotes, condensin I and condensin II are vital for the proper formation and resolution of sister chromosomes. In recent years, evidence has gradually demonstrated that condensins are much more than architects of chromatin struc‐ ture; they are also important regulators of gene transcription. However, the vital role of con‐ densins makes the study of these complexes difficult. In this chapter, the authors introduce several different methods to investigate the roles of condensins in chromatin structure change and gene regulation. A special focus is placed on two particular examples of conden‐ sin in regulating gene transcription: dosage compensation in C. elegans and thymocyte de‐

Id2 (inhibitor of DNA binding 2, dominant-negative helix-loop-helix protein) belongs to a family of helix-loop-helix proteins which plays a central role in the regulation of cell growth and differentiation and cancer. In chapter 5 "The Role of Id2 in the Regulation of Chroma‐ tin Structure and Gene Expression" written by Elena R. Garcia-Trevijano, Luis Torres, Rosa Zaragozá and Juan R. Viña, the authors give a broad introduction to the topic. This chap‐ ter begins with description of the structure and functions of Id2 protein followed by the molecular mechanisms underlying the role of Id2 as a proliferative factor in normal cell

view on molecular mechanisms of chromatin remodeling regulated by sumoylation.

tion mediated by RNA polymerase II.

velopment in mice.

VIII Preface

In section 3 "Chromatin remodeling in DNA damage, development and human disease", four chapters are presented, dealing with the molecular mechanisms underlying the in‐ volvement of chromatin remodeling in controlling key physiological or pathological events such as differentiation, development, DNA damage response, tumorigenesis and microbial infection.

Polycomb group (PcG) proteins are highly conserved regulatory factors that were initially discovered in Drosophila. They constitute a global silencing system and play key roles in embryonic development and stem cell maintenance. Deregulation of PcG members contrib‐ ute to defects in stem cell fates and to tumorigenesis. In mammals, PcG proteins form two main complexes: polycomb-repressive complex 1 and 2 (PRC1, PRC2). They act by modify‐ ing chromatin structure and by regulating deposition and recognition of posttranslational histone modifications.

Chapter 6 "Role of Enhancer of Zeste Homolog 2 Polycomb Protein and Its Significance in Tumor Progression and Cell Differentiation" by Irene Marchesi and Luigi Bagella give an overview of molecular biology and function of PCR2 with special emphasis on EZH2, the catalytic subunit of PRC2. The content covers PCR2-mediated silencing mechanism, PCR2 activity regulation, including expression regulation, posttranscriptional modification and re‐ cruitment to target genes, as well as the mechanisms underlying the role of EZH2 in neuro‐ genesis, skeletal myogenesis and tumorigenesis.

Cells are inescapably and constantly exposed to a variety of environmental and endogenous agents which can cause DNA damage such as single-strand breaks, double-strand breaks, mismatches and base modifications. To maintain genome stability, cells have developed a global signaling network, known as DNA damage response (DDR) to sense and repair DNA damages. Chromatin remodeling is critical during this process, as chromatin constitutes a natural barrier to associated enzymes and regulatory factors to reach DNA. Aging is a com‐ plex process that has long been thought to be a consequence of unprogrammed deleterious events and accumulation of random gene mutation. However, in recent years, DNA damage has been shown to play a central role in premature aging and DNA damage theory of aging has been developed although there are still several unresolved controversies that require further clarification.

In chapter 7 "Chromatin Remodeling in DNA Damage Response and Human Aging" by Lili Gong, Edward Wang and Shiaw-Yih Lin, the authors summarize the current knowledge on DNA damage repair mechanisms, the role of chromatin remodeling in DDR, DDR in hetero‐ chromatin and the interplay between DNA damage, chromatin remodeling and human ag‐ ing. Intracellular pathogens, through a long-standing coexistence with host cells, have evolved mechanisms that provide pathogens with the amazing capacity to adapt and sur‐ vive in variable and often hostile environments encountered in their hosts. The concept of chromatin modification as a mechanism by which pathogens affect host immune responses to facilitate infection has emerged in recent years.

In chapter 8 "Chromatin Remodeling During Host-Bacterial Pathogen Interaction" written by Yong Zhong Xu, Cynthia Kanagaratham and Danuta Radzioch, the chromatin modifica‐ tions in host cells induced by bacterial pathogens and their effects on host gene expression and infection are introduced. MAPK, IFN- and transcription factor NF-κB signaling path‐ ways are common targets for bacteria-induced posttranscriptional modifications. These sig‐ nal pathways selectively affect histone modifications at host target genes therefore affecting the expression of target genes. In this chapter, the potential role of HDAC inhibitors to be used as therapeutic immunomodulators in treatment of infections is also discussed. Defects in epigenetic mechanisms can give rise to several neurological and behavioral phenotypes. Rett syndrome is a pervasive neurodevelopmental disorder that is primarily caused by mu‐ tations in MECP2 gene encoding methyl-CpG-binding protein 2 (MeCP2 protein). The func‐ tions of this protein are related to DNA methylation process, a key epigenetic mechanism which plays a critical role in gene silencing during chromatin remodeling. Rett syndrome is the first human disorder that shows a link between epigenetic modifications/ chromatin re‐ modeling and neuronal dysfunction.

In chapter 9 "Rett Syndrome", the author Daniela Zahorakova gives a detailed description of the clinical features, diagnosis, as well as the molecular mechanism of Rett syndrome that arises as a consequence of MECP2 gene mutations and disordered chromatin remodeling

I would like to thank Ms. Mirna Cvijic of InTech publisher for helping me on this project, to all the authors of the chapters for their time and effort to contribute to this book. I hope readers will enjoy reading this collection of reviews and research papers, leaving with a sense of anticipation for what lies ahead in the field of chromatin remodeling.

> **Dr. Danuta Radzioch** Professor, McGill University Department of Medicine and Department of Human Genetics Montreal, Canada

**Section 1**

**Molecular Basis for Chromatin Structure and**

**Regulation**

**Molecular Basis for Chromatin Structure and Regulation**

In chapter 8 "Chromatin Remodeling During Host-Bacterial Pathogen Interaction" written by Yong Zhong Xu, Cynthia Kanagaratham and Danuta Radzioch, the chromatin modifica‐ tions in host cells induced by bacterial pathogens and their effects on host gene expression and infection are introduced. MAPK, IFN- and transcription factor NF-κB signaling path‐ ways are common targets for bacteria-induced posttranscriptional modifications. These sig‐ nal pathways selectively affect histone modifications at host target genes therefore affecting the expression of target genes. In this chapter, the potential role of HDAC inhibitors to be used as therapeutic immunomodulators in treatment of infections is also discussed. Defects in epigenetic mechanisms can give rise to several neurological and behavioral phenotypes. Rett syndrome is a pervasive neurodevelopmental disorder that is primarily caused by mu‐ tations in MECP2 gene encoding methyl-CpG-binding protein 2 (MeCP2 protein). The func‐ tions of this protein are related to DNA methylation process, a key epigenetic mechanism which plays a critical role in gene silencing during chromatin remodeling. Rett syndrome is the first human disorder that shows a link between epigenetic modifications/ chromatin re‐

In chapter 9 "Rett Syndrome", the author Daniela Zahorakova gives a detailed description of the clinical features, diagnosis, as well as the molecular mechanism of Rett syndrome that arises as a consequence of MECP2 gene mutations and disordered chromatin remodeling

I would like to thank Ms. Mirna Cvijic of InTech publisher for helping me on this project, to all the authors of the chapters for their time and effort to contribute to this book. I hope readers will enjoy reading this collection of reviews and research papers, leaving with a

**Dr. Danuta Radzioch**

Montreal, Canada

Professor, McGill University

Department of Medicine and Department of Human Genetics

sense of anticipation for what lies ahead in the field of chromatin remodeling.

modeling and neuronal dysfunction.

X Preface

**Chapter 1**

**Chromatin Remodelers and Their Way of Action**

Chromatin is the packaged form of the eukaryotic genome in the cell nucleus, presenting the substrate for all DNA dependent processes. The basic packaging unit of chromatin is the nucleosome core, a nucleoprotein structure consisting of 8 histone proteins and 147 bp of DNA. Two of each H2A and H2B, H3 and H4, form an octameric, disc like particle on which 1.65 turns of DNA is wrapped [1]. Nucleosomal cores are separated by a linker DNA, with a varying length of 7 bp to 100 bp, with distinct lengths in different organisms and tissues. Even within one cell type the linker length can vary about 40 bp between the actively transcribed and

Binding of the DNA to the histone octamer and the bending of the molecule on the protein surface present a strong barrier to sequence specific recognition of the nucleosomal DNA molecule. That's why the packaging of DNA into nucleosomes and higher order structures is generally inhibitory to all kind of DNA dependent processes. To overcome DNA sequence accessibility problems, cells have developed mechanisms to open higher order structures of chromatin and to disrupt nucleosomes allowing the binding of sequence specific regulators. In general, two major mechanisms exist which regulate chromatin accessibility: First, histones can be posttranslationally modified and recruit specific effector proteins to chromatin [3]. Second, specific chromatin remodeling enzymes displace the histone octamers from DNA or translocate them on DNA, thereby exposing or protecting underlying DNA sequences to

The presence of 53 different chromatin remodeling enzymes in the human cell suggests specialized functions of these enzymes and the associated complexes. Chromatin remodelers are DNA translocases that apply an ATP-dependent torsional strain to DNA, providing the force to reposition nucleosomes; i.e. moving the histone octamer to a different site on the DNA [4,5]. Diverse remodeling enzymes and complexes have distinct nucleosome positioning

and reproduction in any medium, provided the original work is properly cited.

© 2013 Manelyte and Längst; licensee InTech. This is an open access article 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.

© 2013 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,

regulatory factors that control the DNA dependent processes [4].

Laura Manelyte and Gernot Längst

http://dx.doi.org/10.5772/55683

**1. Introduction**

repressed genes [2].

Additional information is available at the end of the chapter
