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Understanding mechanisms of gene regulation that are independent of the DNA sequence itself – epigenetics – has the potential to overthrow long-held views on central topics in biology, such as the biology of disease or the evolution of species. High throughput technologies reveal epigenetic mechanisms at a genome-wide level, giving rise to epigenomics as a new discipline with a distinct set of research questions and methods. Leading experts from academia, the biotechnology and pharmaceutical industries explain the role of epigenomics in a wide range of contexts, covering basic chromatin biology, imprinting at a genome-wide level, and epigenomics in disease biology and epidemiology. Details on assays and sequencing technology serve as an up-to-date overview of the available technological tool kit. A reliable guide for newcomers to the field as well as experienced scientists, this is a unique resource for anyone interested in applying the power of twenty-first-century genomics to epigenetic studies.
List of contributors
Foreword
Preface
Part I. Basics of Chromatin Biology and Biochemistry
1. Introduction to epigenomics
2. Epigenetics and its historical perspectives
3. Functional networks of human epigenetic factors
4. Nucleosome positioning in promoters: significance and open questions
5. Chemical reporters of protein methylation and acetylation
6. Long non-coding RNA in epigenetic gene silencing
Part II. Epigenomic Imprinting and Stem Cells
7. Active DNA demethylation - the enigma starts in the zygote
8. Histone modifications of lineage specific genes in human embryonic stem cells during in vitro differentiation
9. Epigenetic stability of human pluripotent stem cells
10. Impact of CpG methylation in addressing adipose derived stem cell differentiation towards the cardiac phenotype
11. Regulation of stem cell epigenome by REST
12. MicroRNAs in embryonic stem cells
13. Regulation of timing of replication
Part III. Epigenomic Assays and Sequencing Technology
14. Detection of CpG methylation patterns by affinity capture methods
15. Genome-wide ChIP-DSL profiling of promoter methylation patterns associated with cancer and stem cell differentiation
16. Quantitative, high-resolution CpG methylation assays on the pyrosequencing platform
17. DNA methylation profiling using Illumina BeadArray platform
18. Advances in capillary electrophoresis-based methods for DNA methylation analysis
19. Genome-wide methylome analysis based on new HT sequencing technology
20. 3-D quantitative DNA methylation imaging for chromatin texture analysis in pharmacoepigenomics and toxicoepigenomics
Part IV. Epigenomics in Disease Biology
21. Cancer classification by genome-wide and quantitative DNA methylation analyses
22. Promoter CpG island methylation in colorectal cancer: biology and clinical applications
23. The epigenetic profile of bladder cancer
24. Genome-scale DNA methylation analyses of cancer in children
25. The epigenetics of facioscapulohumeral muscular dystrophy
26. Modulating histone acetylation with inhibitors and activators
Part V. Epigenomics in Neurodegenerative Diseases
27. Study design considerations in epigenetic studies of neuropsychiatric disease
28. Epigenetic regulation in human neurodevelopmental disorders including autism, Rett syndrome and epilepsy
29. The neurobiology of chromatin-associated mechanisms in the context of psychosis and mood spectrum disorders
30. Genome-wide DNA methylation analysis in patients with familial ATR-X mental retardation syndrome
31. Kinases and phosphatases in the epigenetic regulation of cognitive functions
Part VI. Epigenetic Variation, Polymorphism and Epidemiological Perspectives
32. Epigenetic effects of childhood abuse on the human brain
33. X-linked expressed SNPs and dosage compensation
34. Epigenomic diversity of colorectal cancer
35. Epigenetic epidemiology: transgenerational responses to the environment
Index
Krishnarao Appasani is the Founder and Chief Executive Officer of GeneExpression Systems, a conference producing organization focusing on Biomedical and Physical Sciences. He is editor of MicroRNAs: From Basic Science to Disease Biology (2007) and RNA Interference: From Basic Science to Drug Development (2005), also published by Cambridge University Press.
"This is an excellent work, highly readable and well documented by more than a hundred scientists from academia and industry. The extensive coverage of current theory, new technologies, and disease mechanisms, all associated with epigenomics, make this book invaluable to students and researchers in a wide range of disciplines. Recommended for all academic libraries."
- Atsuo Ogura, RIKEN BioResource Center
"Congratulations on a great book! It is a very impressive collection of high-quality contributions in several relevant areas of epigenetics. I enjoyed reading it and I am sure that it will be a very useful resource for everyone in the epigenetics field. I will definitely recommend it to my colleagues!"
- Karl Ekwall, Karolinska Institute
"[...] Appasani gathers our present knowledge about epigenomics in this interesting book. The topics covered will allow the reader to understand the role of epigenetic mechanisms in cell biology and disease. At the same time, this book offers a good opportunity to learn about the epigenomic techniques applied in both basic research and in biotechnology and biomedical companies."
- Marian Martinez-Balbas, CSIC-Barcelona Molecular Biology Institute
"[...] provides a broad coverage of the key aspects of epigenetics and its future potential to treat epigenetic related diseases. I recommend this book as an excellent up-to-date reference for established investigators in the field of epigenomics and to newcomers who want an update of the recent developments in this field. The book can also serve as a reference text for students as part of an advanced course on molecular biology."
- Richard L. Momparler, University of Montréal
"This book is an excellent update on the current status of epigenomics, a relatively new discipline of life sciences bridging genetics and epigenetics [...] The book covers the different aspects from basic science to available technology and highlights the significant impact of epigenomics on the understanding of human disease. Epigenetic abnormalities are very critical in the pathogenesis of human cancer; the understanding of epigenetics is of importance for the development of innovative therapeutics including the potential pharmaceutical use of (pluripotent) stem cells. Experts in their field provide up-to-date information making the book very valuable [...]"
- Christine Guenther, Apceth GmbH and Co. KG, Munich
