Methylation is a reversible covalent chemical modification of DNA intended to regulate gene expression, genome stability, and chromatin structure. Although there are various methods of methylation analysis, most of them are either laborious or expensive, or both. Here, we describe a quick, inexpensive method for analysis of global genome methylation using a cytosine extension assay. The assay can be used for analysis of the total level of CpG, CNpG, and asymmetrical methylation in a given cell culture or in a plant tissue sample.
Global genome methylation Cytosine-extension CpG CNpG Asymmetrical methylation
This is a preview of subscription content, log in to check access.
Springer Nature is developing a new tool to find and evaluate Protocols. Learn more
Finnegan EJ, Genger RK, Peacock WJ, Dennis ES (1998) DNA methylation in plants. Annu Rev Plant Physiol Plant Mol Biol 49:223–247CrossRefPubMedGoogle Scholar
Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol 13:421–426CrossRefPubMedGoogle Scholar
Engler P, Weng A, Storb U (1993) Influences of CpG methylation and target spacing on V(D)J recombination in a transgenic substrate. Mol Cell Biol 13:571–577PubMedGoogle Scholar
Bender J (1998) Cytosine methylation of repeated sequences in eukaryotes: the role of DNA pairing. Trends Biochem Sci 23:252–256CrossRefPubMedGoogle Scholar
Bassing CH, Swat W, Alt FW (2002) The mechanism and regulation of chromosomal V(D)J recombination. Cell 109:S45-S55CrossRefPubMedGoogle Scholar
Shi H, Wang MX, Caldwell CW (2007) CpG islands: their potential as biomarkers for cancer. Expert Rev Mol Diagn 7:519–531CrossRefPubMedGoogle Scholar
Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J (2007) Transge-nerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130:851–862CrossRefPubMedGoogle Scholar
Ingelbrecht I, Van Houdt H, Van Montagu M, Depicker A (1994) Posttranscriptional silencing of reporter transgenes in tobacco correlates with DNA methylation. Proc Natl Acad Sci U S A 91:10502–10526CrossRefPubMedGoogle Scholar
Meyer P, Niedenhof I, ten Lohuis M (1994) Evidence for cytosine methylation of non-symmetrical sequences in transgenic Petunia hybrida. EMBO J 13:2084–2088PubMedGoogle Scholar
Pogribny I, Yi P, James SJ (1999) A sensitive new method for rapid detection of abnormal methylation patterns in global DNA and within CpG islands. Biochem Biophys Res Commun 262:624–628CrossRefPubMedGoogle Scholar
Fujiwara H, Ito M (2002) Nonisotopic cytosine extension assay: a highly sensitive method to evaluate CpG island methylation in the whole genome. Anal Biochem 307:386–389CrossRefPubMedGoogle Scholar
Basnakian AG, James SJ (1996) Quantification of 3′OH DNA breaks by random oligonucleotide-primed synthesis (ROPS) assay. DNA Cell Biol 15:255–262CrossRefPubMedGoogle Scholar