List of Contributors ......................................... V
Preface ..................................................... XI
Part I Introduction to Epigenetics and Epigenetic Methods ...... 1
Early Life Environment, DNA Methylation and Behaviour ........... 3
Moshe Szyf
2 Concepts in Histone Acetyltransferase Biology ............... 25
Anne K. Voss and Tim Thomas
3 Murine Models of Transgenerational Epigenetic Inheritance ... 51
Jennifer E. Cropley and Catherine M. Suter
4 The Molecular Mechanisms of Mammalian X Inactivation ........ 67
Marnie E. Blewitt and Linden J. Gearing
5 Epigenetic Memory in Plants: Polycomb-group Regulation of
Responses to Low Temperature ................................ 83
Sandra N. Oliver and E. Jean Finnegan
6 Centromeres and Telomeres ................................... 99
Emma L. Northrop and Lee H. Wong
7 DNA Sequence Contribution to Nucleosome Distribution ....... 133
Justin A. Fincher and Jonathan H. Dennis
8 Macrosatellite Epigenetics ................................. 143
Brian P. Chadwick
9 Histones: Dosage and Degradation ........................... 161
Rakesh Kumar Singh, Johanna Paik and Akash Gunjan
10 The Epigenetic Basis of Cell Fate Specification and
Reprogramming .............................................. 183
Hongchang Cui
11 DNA Methylation Changes in Cancer .......................... 195
Samson Mani and Zdenko Herceg
12 Variant Histones H2A and Cancer Development ................ 211
Danny Rangasamy
13 5-Methylcytosine as a Modification in RNA .................. 227
Jeffrey E. Squires and Thomas Preiss
14 Paramutation in Plants ..................................... 237
Mario A. Arteaga-Vazquez and Ana E. Dorantes-Acosta
15 Lessons from DNMT3L-dependent Methylation During
Gametogenesis .............................................. 255
Sarah A. Kinkel and Hamish S. Scott
16 Non-coding RNA: an Overview ................................ 271
Alka Saxena and Piero Carninci
Part II Epigenetic Techniques ................................. 291
17 Bisulfite-enabled Technologies ............................. 293
Miina Ollikainen
18 Methylation-sensitive High Resolution Melting for the
Rapid Analysis of DNA Methylation .......................... 325
Thomas Mikeska and Alexander Dobrovic
19 Microarray Mapping of Nucleosome Position .................. 337
Brian Spetman, Sarah Lueking, Brooke Roberts Druliner and
Jonathan H. Dennis
20 Enzymatic Approaches for Genome DNA Methylation
Profiling .................................................. 349
Benjamin Chanrion, Yurong Xin and Fatemeh Haghighi
21 ChIP Sequencing ............................................ 357
Sebastian Lunke and Assam El-Osta
22 Genome-wide DNA Methylation Analysis ....................... 371
Marcel W. Coolen and Susan J. Clark
Part III Epigenetics Reference Manual ......................... 393
23 Bioinformatics Analysis of Epigenomic Methylation
Patterns in the Era of Massively Parallel Sequencing ....... 395
Mark D. Robinson, Bryan Beresford-Smith, Anthony Kaspi
and Izhak Haviv
24 Genetic Resources for the Study of Epigenetic Gene
Regulation in Maize ........................................ 409
Andre Irsigler and Karen M. McGinnis
25 Online Resources and Tools for Epigeneticists .............. 421
Nicholas C. Wong
26 Educational Resources for Epigenetics ...................... 435
Yuk Jing Loke and Jeffrey M. Craig
Index ...................................................... 447
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