Abstract
Epigenetic modifications on the DNA sequence (DNA methylation) or on chromatin-associated proteins (i.e., histones) comprise the “cellular epigenome”; together these modifications play an important role in the regulation of gene expression. Unlike the genome, the epigenome is highly variable between cells and is dynamic and plastic in response to cellular stress and environmental cues. The role of the epigenome, specifically, the methylome has been increasingly highlighted and has been implicated in many cellular and developmental processes such as embryonic reprogramming, cellular differentiation, imprinting, X chromosome inactivation, genomic stability, and complex diseases such as cancer. Over the past decade several methods have been developed and applied to characterize DNA methylation at gene-specific loci (using either traditional bisulfite sequencing or pyrosequencing) or its genome-wide distribution (microarray analysis following methylated DNA immunoprecipitation (MeDIP-chip), analysis by sequencing (MeDIP-seq), reduced representation bisulfite sequencing (RRBS), or shotgun bisulfite sequencing). This chapter reviews traditional bisulfite sequencing and shotgun bisulfite sequencing approaches, with a greater emphasis on shotgun bisulfite sequencing methods and data analysis.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Okano M et al (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99:247–257
Li E et al (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915–926
Bird AP, Wolffe AP (1999) Methylation-induced repression–belts, braces, and chromatin. Cell 99:451–454
Walsh CP et al (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20:116–117
Dodge JE et al (2005) Inactivation of Dnmt3b in mouse embryonic fibroblasts results in DNA hypomethylation, chromosomal instability, and spontaneous immortalization. J Biol Chem 280:17986–17991
Karpf AR, Matsui S (2005) Genetic disruption of cytosine DNA methyltransferase enzymes induces chromosomal instability in human cancer cells. Cancer Res 65:8635–8639
Chen T, Li E (2004) Structure and function of eukaryotic DNA methyltransferases. Curr Top Dev Biol 60:55–89
Jaenisch R, Jahner D (1984) Methylation, expression and chromosomal position of genes in mammals. Biochim Biophys Acta 782:1–9
Surani MA (1998) Imprinting and the initiation of gene silencing in the germ line. Cell 93:309–312
Ng HH, Bird A (1999) DNA methylation and chromatin modification. Curr Opin Genet Dev 9:158–163
Holliday R, Pugh JE (1975) DNA modification mechanisms and gene activity during development. Science 187:226–232
Reik W et al (2003) Mammalian epigenomics: reprogramming the genome for development and therapy. Theriogenology 59:21–32
Metivier R et al (2008) Cyclical DNA methylation of a transcriptionally active promoter. Nature 452:45–50
Gehring M et al (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124:495–506
Kangaspeska S et al (2008) Transient cyclical methylation of promoter DNA. Nature 452:112–115
Frommer M et al (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A 89:1827–1831
Clark SJ et al (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22:2990–2997
Lister R et al (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536
Lister R et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322
Cokus SJ et al (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219
Laurent L et al (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20:320–331
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Hammoud, S.S., Cairns, B.R., Carrell, D.T. (2013). Analysis of Gene-Specific and Genome-Wide Sperm DNA Methylation. In: Carrell, D., Aston, K. (eds) Spermatogenesis. Methods in Molecular Biology, vol 927. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-038-0_39
Download citation
DOI: https://doi.org/10.1007/978-1-62703-038-0_39
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-037-3
Online ISBN: 978-1-62703-038-0
eBook Packages: Springer Protocols