Epigenetic Technological Applications

1st Edition - June 17, 2015
Latest edition
Editor: Yujun George Zheng
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 0 1 0 8 0 - 8
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 0 1 3 2 7 - 4

Epigenetic Technological Applications is a compilation of state-of-the-art technologies involved in epigenetic research. Epigenetics is an exciting new field of biology research,… Read more

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Epigenetic Technological Applications is a compilation of state-of-the-art technologies involved in epigenetic research. Epigenetics is an exciting new field of biology research, and many technologies are invented and developed specifically for epigenetics study. With chapters covering the latest developments in crystallography, computational modeling, the uses of histones, and more, Epigenetic Technological Applications addresses the question of how these new ideas, procedures, and innovations can be applied to current epigenetics research, and how they can keep pushing discovery forward and beyond the epigenetic realm.

List of Contributors
Foreword
Chapter 1. The State of the Art of Epigenetic Technologies
- 1.1 Epigenetics and Chromatin Function
- 1.2 Mechanisms of Epigenetic Regulation
- 1.3 Technologies are Critical for the Advancement of Epigenetic Discovery
- 1.4 Epigenetic Inhibitors as Novel Therapeutics
- 1.5 Perspective
- Acknowledgments
- References
Chapter 2. Technologies for the Measurement and Mapping of Genomic 5-Methylcytosine and 5-Hydroxymethylcytosine
- 2.1 Introduction
- 2.2 Measuring Genomic Levels of 5-Methylcytosine and 5-Hydroxymethylcytosine
- 2.3 Locus-Specific Analysis of 5-Methylcytosine and 5-Hydroxymethylcyotsine
- 2.4 Technologies for Genome-Wide Analysis of 5-Methylcytosine and 5-Hydroxymethylcytosine
- 2.5 Conclusions
- Acknowledgments
- References
Chapter 3. High-Throughput Sequencing-Based Mapping of Cytosine Modifications
- 3.1 Introduction
- 3.2 Cytosine Modifications
- 3.3 High-Throughput Sequencing Methods for Detecting Cytosine Modifications
- 3.4 Conclusions
- References
Chapter 4. Application of Mass Spectrometry in Translational Epigenetics
- 4.1 Introduction
- 4.2 Applications of Mass Spectrometry in Epigenetic Research
- 4.3 Conclusion
- References
Chapter 5. Techniques Analyzing Chromatin Modifications at Specific Single Loci
- 5.1 Gene Expression Pattern is Related to the Covalent Modification of Core Histones
- 5.2 Heterochromatin is Tightly Packed to Repress Gene Expression via Interaction of HP1 and Histone H3 Lys9 Methylation
- 5.3 In Situ Observation of Chromatin Reorganization During Transcription Activation
- 5.4 Chromatin Immunoprecipitation
- 5.5 Cross-Linking Chromosome Immunoprecipitation as a Powerful Tool to Investigate Sequential Recruitment of Histone Acetyltransferase and SWI/SNF Chromatin-Remodeling Complex to the Promoters
- 5.6 Convergence of Bioinformatics and Biophysics Techniques at Observation in Live Single Cell
- 5.7 Future Perspectives: Epigenome Engineering and Manipulating at Specific Genomic Loci in Mammalian Cells
- References
Chapter 6. Comprehensive Analysis of Mammalian Linker-Histone Variants and Their Mutants
- 6.1 Introduction
- 6.2 Linker Histone H1 and Its Variants
- 6.3 Expression Analysis of Mammalian Linker Histone H1 Variants
- 6.4 Genetic Analysis of H1 Variants by Gene Inactivation
- 6.5 In Vivo Tagging and Genome-Wide Mapping of H1 Variants
- 6.6 Mutation Analysis of Histone H1
- 6.7 Conclusion
- References
Chapter 7. Crystallography-Based Mechanistic Insights into Epigenetic Regulation
- 7.1 Introduction
- 7.2 Development of X-ray Crystallography
- 7.3 Key Epigenetic Projects Solved by X-ray Crystallography
- 7.4 Application of X-ray Crystallography in Epigenetic Drug Discovery
- 7.5 Fragment-Based Drug Discovery
- 7.6 Conclusion
- Acknowledgments
- References
Chapter 8. Chemical and Genetic Approaches to Study Histone Modifications
- 8.1 Eukaryotic Chromatin and Histones
- 8.2 The Challenging Diversity of Histone Posttranslational Modifications
- 8.3 A Chemical Biology Approach to Investigate Histone Modifications
- 8.4 Strategies of Native Chemical and Expressed Protein Ligation
- 8.5 Thialysine Analogs of Methylated and Acetylated Histones
- 8.6 Genetic Incorporation of Modified Amino Acids in Histones
- 8.7 Biochemical and Biophysical Studies of Histone Ubiquitylation
- 8.8 Biochemical and Biophysical Studies of Histone Methylation
- 8.9 Outlook
- Acknowledgments
- References
Chapter 9. Peptide Microarrays for Profiling of Epigenetic Targets
- 9.1 Introduction
- 9.2 Applications of Histone Peptide Microarrays
- 9.3 Conclusion and Outlook
- Acknowledgments
- References
Chapter 10. Current Methods for Methylome Profiling
- 10.1 Introduction
- 10.2 Labeling Protein Methylation
- 10.3 Recognizing and Enriching Methylome
- 10.4 Choices of Processing Methylome Sample
- 10.5 Deconvolution of Methylome Sample
- 10.6 Detection Methods for Methylome Profiling
- 10.7 Bioinformatics of Methylome
- 10.8 Examples of Integrative Modules for Methylome Profiling
- 10.9 Perspective
- Acknowledgments
- References
Chapter 11. Bioinformatics and Biostatistics in Mining Epigenetic Disease Markers and Targets
- 11.1 Introduction
- 11.2 Acquisition and Processing of High-Throughput Epigenomic Data
- 11.3 Bioinformatics and Biostatistics in Mining Epigenetic Biomarkers
- 11.4 Bioinformatics and Biostatistics in Mining Epigenetic Disease Targets
- 11.5 Useful Bioinformatic Resources
- 11.6 Conclusions and Future Perspectives
- References
Chapter 12. Computational Modeling to Elucidate Molecular Mechanisms of Epigenetic Memory
- 12.1 Introduction
- 12.2 Identify Puzzle from Experimental Studies
- 12.3 Formulate Mathematical Model
- 12.4 Choose Appropriate Modeling Techniques
- 12.5 Determine Model Parameters
- 12.6 Perform Computational Studies
- 12.7 Identify Insights from Model Studies and Make Testable Predictions
- 12.8 Conclusion
- References
Chapter 13. DNA Methyltransferase Inhibitors for Cancer Therapy
- 13.1 Introduction
- 13.2 Development of DNMTi as Cancer Therapy
- 13.3 Advances in Experimental Methods
- 13.4 Progress on the Identification of Novel DNMTi
- 13.5 Advances in Computational Studies
- 13.6 Data Resources for DNMTi
- 13.7 Conclusions
- Acknowledgments
- References
Chapter 14. Histone Acetyltransferases: Enzymes, Assays, and Inhibitors
- 14.1 Histone Acetyltransferases
- 14.2 The Pharmacologic Significance of HATs
- 14.3 HAT Biochemical Assays
- 14.4 HAT Inhibitors
- 14.5 Conclusion and Perspective
- Acknowledgments
- References
Chapter 15. In Vitro Histone Deacetylase Activity Screening: Making a Case for Better Assays
- 15.1 Introduction
- 15.2 Overview of HDAC Assays
- 15.3 Fluorogenic HDAC Activity Assay
- 15.4 Disadvantages of HDAC Fluorogenic Assays
- 15.5 HDAC Assay Using the Self-Assembled Mono-Layers for Matrix-Assisted Laser
- 15.6 Comparison of the Fluorogenic and SAMDI-MS HDAC Assays – Our Experience
- 15.7 Conclusion
- References
Chapter 16. Enzymatic Assays of Histone Methyltransferase Enzymes
- 16.1 Introduction
- 16.2 Enzymatic Assays for Histone Methyltransferases
- 16.3 Conclusions
- References
Chapter 17. Histone Methyltransferase Inhibitors for Cancer Therapy
- 17.1 Introduction
- 17.2 Histone Lysine Methyltransferases
- 17.3 Protein Arginine Methyltransferases
- 17.4 Conclusion
- References
Chapter 18. Discovery of Histone Demethylase Inhibitors
- 18.1 Introduction
- 18.2 Histone Demethylases and Their Involvement in Disease
- 18.3 Assays for Histone Demethylases and Their Role in the Discovery of Inhibitors
- 18.4 Structural Aspects of Inhibitor Binding
- 18.5 Conclusion
- Acknowledgments
- References
Chapter 19. Histone Demethylases: Background, Purification, and Detection
- 19.1 Introduction
- 19.2 Purification of KDMs
- 19.3 In Vitro Assays to Evaluate Demethylase Activity
- 19.4 In vivo Detection of KDM Activity in Cell Culture Models
- 19.5 Conclusion
- Acknowledgments
- References
Chapter 20. Animal Model Study of Epigenetic Inhibitors
- 20.1 Introduction
- 20.2 Epigenetic Inhibitors
- 20.3 Use of Animal Model to Study the Inhibitors
- 20.4 Perspective and Conclusion
- References
Index

Life Sciences

Physical Sciences & Engineering

Social Sciences & Humanities

Health

Epigenetic Technological Applications

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Yujun George Zheng

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