Abstract
Transposable elements (TE) comprise half of the human genome. LINE-1 and ALU are the most common TE, and they have been used to assess changes in the DNA methylation of repetitive elements in response to intrinsic and extrinsic cellular events. Pyrosequencing® is a real-time sequencing technology that enables quantitative assessment of TE methylation at single-base resolution. In Pyrosequencing, a region of interest is first amplified from bisulfite-converted DNA by polymerase chain reaction (PCR), before PCR amplicons are rendered single stranded and annealed with the Pyrosequencing primer prior to sequencing. In this chapter, we provide an overview of the analysis of repetitive element DNA methylation by bisulfite Pyrosequencing, and we describe a protocol that can be used for such purposes.
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References
Lander ES, Linton LM, Birren B, International Human Genome Sequencing C et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Byun HM, Motta V, Panni T et al (2013) Evolutionary age of repetitive element subfamilies and sensitivity of DNA methylation to airborne pollutants. Parti Fibre Toxicol 10:28
Su J, Shao X, Liu H et al (2012) Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics 99:10–17
Choi SH, Worswick S, Byun HM et al (2009) Changes in DNA methylation of tandem DNA repeats are different from interspersed repeats in cancer. Int J Cancer 125:723–729
Guo L, Byun HM, Zhong J et al (2014) Effects of short-term exposure to inhalable particulate matter on DNA methylation of tandem repeats. Environ Mol Mutagen 55:322–335
Florea A-M (2013) DNA methylation pyrosequencing assay is applicable for the assessment of epigenetic active environmental or clinical relevant chemicals. Biomed Res Int 2013:486072
Lai RK, Chen Y, Guan X et al (2014) Genome-wide methylation analyses in glioblastoma multiforme. PloS One 9:e89376
Yang AS, Estecio MR, Doshi K et al (2004) A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 32:e38
Baccarelli A, Wright R, Bollati V et al (2010) Ischemic heart disease and stroke in relation to blood DNA methylation. Epidemiol 21:819–828
Zhu ZZ, Hou L, Bollati V et al (2012) Predictors of global methylation levels in blood DNA of healthy subjects: a combined analysis. Int J Epidemiol 41:126–139
Wagner I, Capesius I (1981) Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography. Biochim Biophys Acta 654:52–56
Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89–92
Baba Y, Huttenhower C, Nosho K et al (2010) Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors. Mol Cancer 9:125
Lisanti S, Omar WA, Tomaszewski B et al (2013) Comparison of methods for quantification of global DNA methylation in human cells and tissues. PloS One 8:e79044
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Tabish, A.M., Baccarelli, A.A., Godderis, L., Barrow, T.M., Hoet, P., Byun, HM. (2015). Assessment of Changes in Global DNA Methylation Levels by Pyrosequencing® of Repetitive Elements. In: Lehmann, U., Tost, J. (eds) Pyrosequencing. Methods in Molecular Biology, vol 1315. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2715-9_15
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DOI: https://doi.org/10.1007/978-1-4939-2715-9_15
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2714-2
Online ISBN: 978-1-4939-2715-9
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