Table Of ContentDNA METHYLATION –
FROM GENOMICS
TO TECHNOLOGY
Edited by Tatiana Tatarinova
and Owain Kerton
DNA Methylation – From Genomics to Technology
Edited by Tatiana Tatarinova and Owain Kerton
Published by InTech
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First published March, 2012
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DNA Methylation – From Genomics to Technology,
Edited by Tatiana Tatarinova and Owain Kerton
p. cm.
ISBN 978-953-51-0320-2
Contents
Preface IX
Part 1 Epigenetics Technology and Bioinformatics 1
Chapter 1 Modelling DNA Methylation Dynamics 3
Karthika Raghavan and Heather J. Ruskin
Chapter 2 DNA Methylation Profiling
from High-Throughput Sequencing Data 29
Michael Hackenberg, Guillermo Barturen
and José L. Oliver
Chapter 3 GC Biology in Eukaryotes and Prokaryotes 55
3
Eran Elhaik and Tatiana Tatarinova
Chapter 4 Inheritance of DNA Methylation in Plant Genome 69
Tomoko Takamiya, Saeko Hosobuchi,
Kaliyamoorthy Seetharam, Yasufumi Murakami
and Hisato Okuizumi
Chapter 5 MethylMeter®: A Quantitative,
Sensitive, and Bisulfite-Free Method
for Analysis of DNA Methylation 93
David R. McCarthy, Philip D. Cotter, and Michelle M. Hanna
Part 2 Human and Animal Health 117
Chapter 6 DNA Methylation in Mammalian
and Non-Mammalian Organisms 119
Michael Moffat, James P. Reddington,
Sari Pennings and Richard R. Meehan
Chapter 7 Could Tissue-Specific Genes be Silenced in Cattle
Carrying the Rob(1;29) Robertsonian Translocation? 151
Alicia Postiglioni, Rody Artigas, Andrés Iriarte,
Wanda Iriarte, Nicolás Grasso and Gonzalo Rincón
VI Contents
Chapter 8 Epigenetic Defects Related Reproductive Technologies:
Large Offspring Syndrome (LOS) 167
Makoto Nagai, Makiko Meguro-Horike
and Shin-ichi Horike
Chapter 9 Aberrant DNA Methylation of Imprinted Loci
in Male and Female Germ Cells of Infertile Couples 183
Takahiro Arima, Hiroaki Okae, Hitoshi Hiura,
Naoko Miyauchi, Fumi Sato, Akiko Sato
and Chika Hayashi
Chapter 10 DNA Methylation and
Trinucleotide Repeat Expansion Diseases 193
Mark A. Pook
Part 3 Methylation Changes and Cancer 209
Chapter 11 Investigating the Role DNA Methylations Plays
in Developing Hepatocellular Carcinoma Associated
with Tyrosinemia Type 1 Using the Comet Assay 211
Johannes F. Wentzel and Pieter J. Pretorius
Chapter 12 DNA Methylation and Histone Deacetylation:
Interplay and Combined Therapy in Cancer 227
Yi Qiu, Daniel Shabashvili, Xuehui Li, Priya K. Gopalan,
Min Chen and Maria Zajac-Kaye
Chapter 13 Effects of Dietary Nutrients
on DNA Methylation and Imprinting 289
Ali A. Alshatwi and Gowhar Shafi
Chapter 14 Epigenetic Alteration of
Receptor Tyrosine Kinases in Cancer 303
Anica Dricu, Stefana Oana Purcaru, Raluca Budiu,
Roxana Ola, Daniela Elise Tache, Anda Vlad
Chapter 15 The Importance of Aberrant
DNA Methylation in Cancer 331
Koraljka Gall Trošelj, Renata
Novak Kujundžić and Ivana Grbeša
Chapter 16 DNA Methylation in Acute Leukemia 359
Kristen H. Taylor and Michael X. Wang
Preface
The term epigenetic was coined in 1957 by Conrad Hal Waddington, who is
considered to be the last Renaissance biologist. Epigenetics is defined as the study of
changes in gene expression due to mechanisms other than structural changes in DNA;
that is changes arisen are not as a result of a change in the nucleotide sequence.
Epigenetics is consequently used to explain phenomena which cannot be explained by
the result of standard genetic mutations, for example, hereditary changes in gene
expression as a result of environmental factors.
DNA methylation is one example of such a structural change which affects gene
expression. Methylation occurs through the addition of a chemical methyl group (-
CH3) in a covalent bond to the cytosine bases of the DNA backbone and typically
occurs at a Cysteine-phosphate-Guanine- (CpG) dinucleotide1. DNA methylation is
common in humans, where 70 to 80% of CpG dinucleotides are methylated. Generally,
methylation occurs in noncoding sequences subsequently having little effect on gene
expression. Interestingly, in "simple" organisms, such as yeast and fruit fly, there is
little or no DNA methylation.
DNA methyltransferases (DNMTs), are the enzyme family which catalyses the
methylation process which they do by , recognizing palindromic dinucleotides of
CpG. There are a number of different groups of DNMTs and three DNMTs have been
identified to operate in mammals. DNMT1, DNMT3A, and DNMT3B. A fourth similar
enzyme (DNMT2 or TRDMT1) has been identified which is structurally similar to the
other DMNTs, however, it causes no detectable effect on the total DNA methylation,
suggesting that this enzyme has little role in DNA methylation. Interestingly, the
genome of Drosophila contains a single DNMT gene, which most closely resembles
mammalian DNMT2.
DNA methylation of CpG dinucleotides is essential for plant and mammalian
development by mediating the expression of genes and plays a key role in X
inactivation, genomic imprinting, embryonic development, chromosome stability,
chromatin structure and may also be involved in the immobilization of transposons
1 Cause and Consequences of Genetic and Epigenetic Alterations in Human Cancer. Sadikovic, B,
et al. 6, September 2008, Current Genomics, Vol. 9, pp. 394-408
X Preface
and the control of tissue-specific gene expression. DNA methylation also has health
implications, for example the gain or loss of DNA methylation can produce loss of
genomic imprinting and result in diseases such as Beckwith-Wiedermann syndrome,
Prader-Willi syndrome or Angelman syndrome.
Changes in the pattern of DNA methylation are commonly seen in human tumors.
Both genome wide hypomethylation (insufficient methylation) and region-specific
hypermethylation (excessive methylation) have been suggested to play a role in
carcinogenesis2. A common cause of the loss of tumor-suppressor miRNAs in cancer is
the silencing of primary transcripts by CpG island promoter by hypermethylation3.
DNA hypomethylation also contributes to cancer development via three major
mechanisms, such as: an increase in genomic instability, reactivation of transposable
elements and loss of imprinting.
Presence of epigenetic marks enables cells with the same genotype have potential to
display different phenotypes and differentiate into many cell-types with different
functions, and responses to environmental and intercellular signaling. For example,
DNA methylation is essential for the process of imprinting. Imprinted genes are
expressed from only one parental allele. This mono-allelic gene expression is directed
by epigenetic marks established in the mammalian germ line and a single mutation,
either genetic or epigenetic, can cause disease. There is an increased prevalence of
imprinting disorders associated with human assisted reproductive technologies.
This books highlights the methods and mechanisms by which epigenetics with a focus
on DNA methylation can be studied and its impacts on health.
In the first part, the first chapter focuses on the modeling and feedback dynamics of
DNA methylation, discussing mechanisms and controlling factors as well as DNA
sequences pattern analyses and histone modifications and their association with
disease initiation. Most methods for detecting methylated-CpG islands rely on
chemical conversion of DNA by treatment with bisulfite. The second chapter discusses
how DNA bisulfite treatment together with high-throughput sequencing allows
determining the DNA methylation on a whole genome scale at single cytosine
resolution and introduces software for analysis of bisulfite sequencing data. The third
chapter presents analysis of GC3-rich genes that have more methylation targets. The
fourth chapter is dedicated to inheritance of DNA methylation in plant genomes and
introduces restriction landmark genome scanning method - a quantitative approach
for simultaneous assay of methylation status and the fifth chapter presents
MethylMeter, a new bisulfite-free method to detect and quantify DNA methylation is
described and applied to the detection of imprinting disorders. One of the advantages
2 Lengauer, C. DNA Methylation. McGraw-Hill Encyclopedia of Science & Technology. 10. New
York : McGraw-Hill, 2007, Vol. 5
3 Lengauer, C. DNA Methylation. McGraw-Hill Encyclopedia of Science & Technology. 10. New
York : McGraw-Hill, 2007, Vol. 5
