List of contributors ............................................ x
Foreword by Azim Surani ....................................... xxv
Preface ..................................................... xxvii
I Basics of chromatin biology and biochemistry .................. 1
1 Introduction to epigenomics
Krishnarao Appasani and Raghu K. Appasani .................... 3
2 Epigenetics and its historical perspectives
Robin Holliday .............................................. 19
3 Functional networks of human epigenetic factors
Andrey Poleshko, Natalia Shalginskikh, and Richard A. Katz .. 30
4 Nucleosome positioning in promoters: significance and open
questions
Jun S. Song and David E. Fisher ............................. 47
5 Chemical reporters of protein methylation and acetylation
Markus Grammel, Yu-Ying Yang, and Howard C. Hang ............ 60
6 Long non-coding RNA in epigenetic gene silencing
Takashi Nagano .............................................. 73
II Epigenomic imprinting and stem cells ....................... 89
7 Active DNA demethylation: the enigma starts in the zygote
Julia Arand, Konstantin Lepikhov, Mark Wossidlo, and Jörn
Walter ...................................................... 91
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 ...... 104
9 Epigenetic stability of human pluripotent stem cells
Céline Vallot and Claire Rougeulle ......................... 118
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 ....... 134
Contents
11 Regulation of the stem cell epigenome by REST
Angela Bithell and Noel J. Buckley ......................... 146
12 MicroRNAs in embryonic stem cells
Shari Orlanski and Yehudit Bergman ......................... 163
13 Regulation of timing of replication
Rituparna Mukhopadhyay and Eric E. Bouhassira .............. 179
III Epigenomic assays and sequencing technology ............... 195
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 ............................................... 197
15 Genome-wide ChlP-DSL profiling of promoter methylation
patterns associated with cancer and stem cell
differentiation
Jeffrey D. Falk ............................................ 210
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 .................................. 223
17 DNA methylation profiling using Illumina BeadArray
platform
Marina Bibikova, Jian-Bing Fan, and Kevin L. Gunderson ..... 235
18 Advances in capillary electrophoresis-based methods for
DNA methylation analysis
Benjamin G. Schroeder, Victoria L. Boyd, and Gerald Zon .... 249
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 ................................................ 260
20 Three-dimensional quantitative DNA methylation imaging
for chromatin texture analysis in pharmacoepigenomics
and toxicoepigenomics
Jian Tajbakhsh and Arkadiusz Gertych ....................... 273
IV Epigenomics in disease biology ............................. 291
21 Cancer classification by genome-wide and quantitative DNA
methylation analyses
Atsushi Kaneda ............................................. 293
22 Promoter CpG island methylation in colorectal cancer:
biology and clinical applications
Sarah Derks and Manon van Engeland ......................... 306
23 The epigenetic profile of bladder cancer
Ewa Dudziec and James W.F. Catto ........................... 323
24 Genome-scale DNA methylation analyses of cancer in
children
Nicholas C. Wong and David M. Ashley ....................... 338
25 The epigenetics of facioscapulohumeral muscular dystrophy
Weihua Zeng, Alexander R. Ball, Jr., and Kyoko Yokomori .... 347
26 Modulating histone acetylation with inhibitors and
activators
B. Ruthrotha Selvi, D.V. Mohankrishna, and Tapas K. Kundu .. 362
V Epigenomics in neurodegenerative diseases .................. 389
27 Study design considerations in epigenetic studies of
neuropsychiatric disease
Fatemeh Haghighi, Sephorah Zaman, and Yurong Xin ........... 391
28 Epigenetic regulation in human neurodevelopmental
disorders including autism, Rett syndrome, and epilepsy
Laura В.K. Herzing ......................................... 404
29 The neurobiology of chromatin-associated mechanisms in
the context of psychosis and mood spectrum disorders
Schahram Akbarian .......................................... 420
30 Genome-wide DNA methylation analysis in patients with
familial ATR-X mental retardation syndrome
Gemma Carvill and Andrew Sharp ............................. 434
31 Kinases and phosphatases in the epigenetic regulation of
cognitive functions
Tamara B. Franklin and Isabelle M. Mansuy .................. 447
VI Epigenetic variation, polymorphism, and epidemiological
perspectives .................................................. 459
32 Epigenetic effects of childhood abuse on the human brain
Benoit Labonte and Gustavo Turecki ......................... 461
33 X-linked expressed single nucleotide polymorphisms and
dosage compensation
Lygia V. Pereira and Joana C. Moreira de Mello ............. 483
34 Epigenomic diversity of colorectal cancer
Aditi Hazra and Shuji Ogino ................................ 491
35 Epigenetic epidemiology: transgenerational responses to
the environment
Lars Olov Bygren ........................................... 505
Index ......................................................... 514
The colour plates are to be found between pages 162 and 163
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