New developments in chromatin research / Neil M. Simpson and Valerie J. Stewart, editors.

Format:

Book

Contributor:

Simpson, Neil M.

Stewart, Valerie J.

Series:

Genetics--research and issues series.

Cell biology research progress.

Genetics--research and issues

Cell biology research progress

Language:

English

Subjects (All):

Chromatin--Research--Methodology.

Chromatin.

Physical Description:

1 online resource (249 p.)

Edition:

1st ed.

Place of Publication:

New York : Nova Science Publishers, 2012.

Language Note:

English

Summary:

Chromatin is DNA plus the proteins (and RNA) that package DNA within the cell nucleus. The primary functions of chromatin are: to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene expression and DNA replication. In this book, the authors present topical research in the study of chromatin including the varied functions of aurora kinases A and B in mitosis and carcinogenesis; the chromatin state of pluripotent stem cells; MITF meets chromatin in melanoma; the state of chromatin as an integrative indicator of cell stress; analysing DNA damage and its repair throughout entire genomes; the cloning process, structural characterisation of Revolver transposon and its patented application for chromosome tags; DNA damage and Rad16; and glucocorticoid-induced chromatin remodelling.

Contents:

Intro

Library of Congress Cataloging-in-Publication Data

Contents

Preface

The Varied Functions of Aurora Kinases A and B in Mitosis and Carcinogenesis

Abstract

Introduction

Aurora A Kinase

Aurora A Localization

Regulation of Aurora A Protein Levels

Aurora A Mitotic Functions

Aurora A Functions in Mitotic Entry and Centrosomal Regulation

Aurora A Functions in Spindle Assembly

Regulation of Aurora A Activity

Aurora A and Cancer

Aurora B Kinase

Aurora B Localization

Regulation of Aurora B Levels

Regulation of Aurora B Activity

Aurora B Mitotic Functions

Aurora B Functions in Chromosome Structure and Alignment

Aurora B Functions in Chromosome Segregation and Anaphase Onset

Aurora B Functions in Cytokinesis

Aurora B and Cancer

Perspectives - Is there a Signaling Cross-Talk between Aurora A and Aurora B?

Acknowledgments

References

Chromatin Structure and Epigenetics

1. Introduction

2. Chromatin Structure and Nucleosome Dynamics

2.1. DNA Structure and Chromatin Fibers

2.2. Nucleosome Positioning

2.3. Nucleosome Dynamics and Gene Regulation

3. Histone Post-Translational Modifications and Chromatin Structure

3.1. Types of Histone Post-Translational Modifications

3.1.1. Histone Acetylation

3.1.2. Histone Methylation

3.1.3. Other Modifications

3.2. Crosstalk between Histone Post-Translational Modifications

3.3. Distribution of Histone PTMs within Genomic Domains

4. DNA Modifications and Chromatin Structure

4.1. DNA Methylation and Demethylation

4.1.1. DNA Methylation

4.1.2. DNA Demethylation

4.2. Crosstalk between DNA Marks and Histone PTMs

4.3. MBP Function as Chromatin Architectural Proteins

Conclusion

Acknowledgements

Grant Information

References.

Sperm Chromatin Integrity, DNA Fragmentation and Male Fertility

1. Sperm Chromatin Structure

Balhorn's Model

Toroids

Histone Bound DNA

Chromatin Remodelling during Spermatogenesis

Chromosome Territories

2. Sperm Chromatin Integrity, DNA Fragmentation and Male Fertility

Origin of Sperm DNA Fragmentation

Incomplete Repair of DNA Breaks during Chromatin Remodelling

Aberrant Protamination

Defective Apoptosis

Excessive Production of ROS in the Ejaculate

Other Factors

Methods of Evaluation of Sperm DNA Fragmentation

Sperm Chromatin Structure Assay (SCSA)

Terminal Deoxytransferase Mediated deoxyUridine Triphosphate Nick End Labelling (TUNEL)

Comet Assay

Sperm Chromatin Dispersion Test

Impact of Sperm Nuclear Integrity on Male Fertility

Impact of Sperm Nuclear Integrity on Reproduction

Natural Conception

ART Conception

3. Future Perspectives

Fundamental Research Is Essential

Standardization of the Methods for Sperm DNA Damage Evaluation

Questions Concerning Factors Influencing the Predictive Value of SDF

Long-Term Follow Up of ART Children

The Chromatin State of Pluripotent Stem Cells

Regulation of Pluripotency in ESCs

Higher-order Chromatin Architecture in ESCs

Chromatin Structure in ESCs

Chromatin Bivalency in ESCs

ATP-Dependent Chromatin Remodeling

Histone Variants and Exchange of Histones

Role of Chromatin in iPSC Generation

Epigenetic Regulation during iPSC Generation

MITF Meets Chromatin in Melanoma

MITF and Melanoma

The SWI/SNF Complex

SWI/SNF in Differentiation and Cancer

MITF and SWI/SNF in Melanoma

Conflict of Interest

The State of Chromatin as an Integrative Indicator of Cell Stress

A Genomics Approach to Analysing DNA Damage and Its Repair throughout Entire Genomes

Materials and Methods

UV Irradiation

DNA Preparation

Fragmenting DNA by Sonication

Immunoprecipitation (IP)

Repair of DNA Damages Prior to PCR Amplification

PCR Amplification

Labelling

Hybridization

Feature Extraction

Results

Detecting CPDs Throughout the Entire Yeast Genome

Repair of CPDs in Wild Type and rad4 Cells

Discussion

Supplementary Data

Funding

Recent Patent on Revolver-2: A Novel Transposon-Like Gene Useful for Chromosome Tags of Rye

Large Gaps of DNA Markers in the Rye Genome

Rye Genome Specific Transposon-Like

Gene-Family Revolver

Highly Quantitative and Structural

Diversity of Revolver

Chromosome Tags by Using Revolver

Current and Future Development

The Removal of DNA Damage Is Promoted by the Yeast Global Genome Nucleotide Excision Repair Factor Rad16

Plasmids and Yeast Strains

UV Survival Assays

Chromatin Immunoprecipitation (CHIP)

Chromatin Preparation, Mnase Digestion, and the High-Resolution Nucleosome Mapping

Restriction Enzyme Accessibility

Preparation of Radioactive Probes for Southern Blot Analysis

UV Treatment of Yeast Cells, DNA Isolation and High Resolution Mapping of CPD Sites

UV Induced Histone H3 Acetylation (K9, K14) Requires Both Rad7 and Rad16

Rad7 and Rad16 Control H3Ac Status by Regulating Gcn5 Occupancy at MFA2

Histone H3 Acetylation Regulates Chromatin Structure at the Promoter of MFA2

Increased Histone H3 Acetylation Levels at MFA2 in TUP1 Deleted ( Cells Is Dependent on Gcn5 and Rad16.

Increased Chromatin Accessibility at MFA2 in TUP1 Deleted ( Cells Depends on Rad16 and Gcn5

Increased Histone H3 Acetylation Levels and Open Chromatin Structure are Required for Rad7 and Rad16 Independent GG-NER

The Atpase and RING Domains of Rad16 Both Contribute to Efficient UV Survival

The Atpase and RING Domains of Rad16 Are Both Required for UV Induced Gcn5 Occupancy and Histone H3 Acetylation

The Atpase and RING Domains of Rad16 Are Both Required for Efficient GG-NER

Chromatin Condensation in Infertile Sperm

Chromatin Condensation during Spermatogenesis

DNA Packaging in Mammalian Male Germ Cells

Human Male Infertility

Etiology of Sperm DNA Damage

Protamine Deficiency

Apoptosis

Drugs, Chemotherapy, and Radiotherapy

Reactive Oxygen Species

Cigarette Smoking

Post-Testicular Factors

Varicoceles

Mechanisms of Sperm DNA Damage

Evaluation of Sperm DNA Damage

The Comet Assay

Terminal dUTP Nick-End Labeling (TUNEL) Assay

Toluidine Blue Staining

Chromomycin A3 (CMA3) Assay

Ultrastructure of Spermatozoa from Infertile Men

Clinical Significance of Sperm DNA Damage

Glucocorticoid-Induced Chromatin Remodeling: A Novel Molecular Mechanism of Traumatic Stress

Chromatin Remodeling

Chromatin Remodeling, p11 and PTSD

Chromatin, Memory and Depression

Index.

Notes:

Nova biomedical.

Includes bibliographical references and index.

Description based on print version record.

ISBN:

1-62081-832-9

OCLC:

846946083