Epigenomics: From Chromatin Biology to Therapeutics

Dedication
Contents
List of contributors
Foreword • Azim Surani
Preface
Part I: Basics of chromatin biology and biochemistry
	1 Introduction to epigenomics • Krishnarao Appasani and Raghu K. Appasani
	2 Epigenetics and its historical perspectives • Robin Holliday
	3 Functional networks of human epigenetic factors • Andrey Poleshko, Natalia Shalginskikh, and Richard A. Katz
	4 Nucleosome positioning in promoters: significance and open questions • Jun S. Song and David E. Fisher
	5 Chemical reporters of protein methylation and acetylation • Markus Grammel, Yu-Ying Yang, and Howard C. Hang
	6 Long non-coding RNA in epigenetic gene silencing • Takashi Nagano
Part II: Epigenomic imprinting and stem cells
	7 Active DNA demethylation: the enigma starts in the zygote • Julia Arand, Konstantin Lepikhov, Mark Wossidlo, and Jörn Walter
	8 Histone modifications of lineage-specific genes in human embryonic stem cells during in vitro differentiation • Hyemin Kim, Hogyu Seo, Daeyoup Lee, and Yong-Mahn Han
	9 Epigenetic stability of human pluripotent stem cells • Céline Vallot and Claire Rougeulle
	10 Impact of CpG methylation in addressing adipose-derived stem cell differentiation towards the cardiac phenotype • Alice Pasini, Francesca Bonafè, Emanuela Fiumana, Carlo Guarnieri, Paolo G. Morselli, Carlo M. Oranges, Claudio M. Caldarera, Claudio Muscari, and Emanuele Giordano
	11 Regulation of the stem cell epigenome by RESTAngela Bithell and Noel J. Buckley
	12 MicroRNAs in embryonic stem cells • Shari Orlanski and Yehudit Bergman
	13 Regulation of timing of replication • Rituparna Mukhopadhyay and Eric E. Bouhassira
Part III: Epigenomic assays and sequencing technology
	14 Detection of CpG methylation patterns by affinity capture methods • Luis G. Acevedo, Ana Sanz, Dylan Maixner, Kornel Schuebel, Mary A. Jelinek, David Goldman, and Joseph M. Fernandez
	15 Genome-wide ChIP-DSL profiling of promoter methylation patterns associated with cancer and stem cell differentiation • Jeffrey D. Falk
	16 Quantitative, high-resolution CpG methylation assays on the pyrosequencing platform • Dirk Löffert, Ralf Peist, Thea Rütjes, Norbert Hochstein, Dorothee Honsel, Frank Narz, Ioanna Andreou, Richard Kroon, Andreas Missel, Andrea Linnemann-Florl, Lennart Suckau, and Gerald Schock
	17 DNA methylation profiling using Illumina BeadArray platform • Marina Bibikova, Jian-Bing Fan, and Kevin L. Gunderson
	18 Advances in capillary electrophoresis-based methods for DNA methylation analysis • Benjamin G. Schroeder, Victoria L. Boyd, and Gerald Zon
	19 Genome-wide methylome analysis based on new high-throughput sequencing technology • Mingzhi Ye, Fei Gao, Xu Han, Guanyu Ji, Zhixiang Yan, and Honglong Wu
	20 Three-dimensional quantitative DNA methylation imaging for chromatin texture analysis in pharmacoepigenomics andtoxicoepigenomics • Jian Tajbakhsh and Arkadiusz Gertych
Part IV: Epigenomics in disease biology
	21 Cancer classification by genome-wide and quantitative DNA methylation analyses • Atsushi Kaneda
	22 Promoter CpG island methylation in colorectal cancer: biology and clinical applications • Sarah Derks and Manon van Engeland
	23 The epigenetic profile of bladder cancer • Ewa Dudziec and James W. F. Catto
	24 Genome-scale DNA methylation analyses of cancer in children • Nicholas C. Wong and David M. Ashley
	25 The epigenetics of facioscapulohumeral muscular dystrophy • Weihua Zeng, Alexander R. Ball, Jr., and Kyoko Yokomori
	26 Modulating histone acetylation with inhibitors and activators • B. Ruthrotha Selvi, D. V. Mohankrishna, and Tapas K. Kundu
Part V: Epigenomics in neurodegenerative diseases
	27 Study design considerations in epigenetic studies of neuropsychiatricdiseaseFatemeh Haghighi, Sephorah Zaman, and Yurong Xin
	28 Epigenetic regulation in human neurodevelopmental disorders including autism, Rett syndrome, and epilepsy • Laura B. K. Herzing
	29 The neurobiology of chromatin-associated mechanisms in the context of psychosis and mood spectrum disorders • Schahram Akbarian
	30 Genome-wide DNA methylation analysis in patients with familial ATR-X mental retardation syndrome • Gemma Carvill and Andrew Sharp
	31 Kinases and phosphatases in the epigenetic regulation of cognitive functions • Tamara B. Franklin and Isabelle M. Mansuy
Part VI: Epigenetic variation, polymorphism, and epidemiological perspectives
	32 Epigenetic effects of childhood abuse on the human brain • Benoit Labonté and Gustavo Turecki
	33 X-linked expressed single nucleotide polymorphisms and dosage compensation • Lygia V. Pereira and Joana C. Moreira de Mello
	34 Epigenomic diversity of colorectal cancer • Aditi Hazra and Shuji Ogino
	35 Epigenetic epidemiology: transgenerational responses to the environment • Lars Olov Bygren
Index