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Epigenetic modifications act on DNA and its packaging proteins, the histones, to regulate genome function. Manifest as the heritable methylation of DNA and as post-translational histone modifications, these molecular flags influence the architecture and integrity of the chromosome, the accessibility of DNA to gene regulatory components and the ability of chromatin to interact within nuclear complexes. While a multicellular individual has only one genome, it has multiple epigenomes reflecting the diversity of cell types and their properties at different times of life; in health and in disease. Relationships are emerging between the underlying DNA sequence and dynamic epigenetic states and their consequences, such as the role of RNA interference and non-coding RNA. These integrated approaches go hand-in-hand with studies describing the genomic locations of epigenetic modifications in different cell types at different times.
The excitement and curiosity surrounding epigenomics is driven by a growing community of researchers in a burgeoning field and the development of new technologies built on the backbone of genome sequencing projects. Research has shown that the adaptability and vulnerability of epigenetic states has profound effects on natural variation, the response of the genome to its environment and on health and disease. The aim of this volume is not to describe epigenomes, but rather to explore how understanding epigenomes tells us more about how biological systems work and the challenges and approaches taken to accomplish this. These contributions have attempted to integrate epigenomics into our understanding of genomes in wider context, and to communicate some of the wonders of epigenetics illustrated through examples across the biological spectrum.
Preface/Introduction: Introduction to epigenomics, AC Ferguson-Smith, JM Greally, RA Martienssen; Section I -- Epigenomic technologies and analytical approaches1. Strategies for epigenome analysis, AB Brinkman and HG Stunnenberg2. Sequencing the epigenome, A Meissner and BE Bernstein3. Integrating epigenomic Results, S-Y Yoo and RW Doerge4. Visualising the epigenome, P Flicek and E BirneySection II -- Roles of DNA, RNA and chromatin in epigenomics5. The expanding view of cytosine methylation, JM Greally6. Structural and biochemical advances in mammalian DNA methylation, X Cheng and R Blumenthal7. Epigenetic profiling of histone variants, S Henikoff8. Epigenetic phenomena and epigenomics in maize, J Hollick and N Springer9. Epigenetic silencing of pericentric heterochromatin by RNA interference in Schizosaccharomyces pombe, S Locke and RA Martienssen10. Describing epigenomic information in Arabidopsis, I. Henderson11. The role of small RNAs in establishing chromatin architecture in Drosophila, J Birchler12. MacroRNAs in the epigenetic control of X inactivation, S Shibata and JT. LeeSection III -- Epigenetic control of developmental processes13. Polycomb complexes and the role of epigenetic memory in development, Y Schwartz and V Pirrotta14. Genomic imprinting - a model for roles of histone modifications in epigenetic control, K McEwan and AC Ferguson-Smith15. The epigenomic landscape of reprogramming in mammals, G Ficz, C Farthing and W Reik16. Epigenetic regulation -- lessons from globin loci, A Dean and S Fiering17. Meiotic silencing, infertility and X chromosome evolution, J. TurnerSection IV -- The epigenome in health and disease18. Genome defence -- the Neurospora paradigm, M Rountree and E Selker19. Integrating the genome and epigenome in human disease, C Widelius20. A changing epigenome in health and disease, E. Ballestar and M Esteller21. Cancer epigenomics, C. Ladd-Acosta and A Feinberg22. Epigenetic modulation by environmental factors, M Doyle and R Amasino23. The relevance of epigenetics to major psychosis, J Mill and A PetronisIndex